For anyone flying into Cape Town airport, the townships are hard to ignore. Approaching from the northwest, with Robben Island taut as an animal skin in the ocean below you and Table Mountain straight ahead, you swoop round to cruise inland over row upon row of matchbox houses in sunshine-bright colours, while in the distance you can make out the squatter camps - a ramshackle jumble of shacks and sheds under an unappetising blanket of woodsmoke smog.

At ground level, the sprawl is even more in-your-face - just south of the airport are the biggest Cape Flats townships, Khayelitsha and Mitchell's Plain, and on the way into town, shuddering under the constant traffic noise from the N2 highway, are Guguletu and Langa. The squatter camps fringing the townships are said to be growing at a rate of several thousand new arrivals per month, and though roughly built of timber, corrugated iron and plastic sheeting, the roadside shacks look distinctly permanent. Some blocks are marked by lamp posts from which wires fan out like maypole ribbons, connecting the shacks to the mains. Established and conspicuous as these settlements are, it's hard to believe that some middle class Capetonians, comfortably ensconced on the other side of Table Mountain, are practically blind to their existence.

It's thought that very few white South Africans have ever taken a township tour, and the make-up of the group I've joined does nothing to disprove this theory. We number six: three New Zealanders, two Belgians and one Brit.

"This," says Brian, our guide, indicating a broken track to our left, "was Richmond Street." Peering out through the windows of our air-conditioned minibus, we strain to imagine how the street might have looked in its 60s heyday. It used to be busy, Brian tells us, with people hurrying to the post office or the barber's or the grocery shops, and children on their way to school. "At night, you could always hear jazz music, and sometimes voodoo drums."

As a prelude to our township visit, we're driving around District Six, the one expanse of prime real estate in Cape Town that no commercial property developer has been prepared to touch. If the soil could speak, this urban wasteland perched between Table Mountain and the docks would have plenty of stories to tell - but it's deserted, and eerily silent. There's little to see apart from rubble-strewn grassland and a few marooned churches and mosques. Still, the reason for coming here is not so much to see what's here now, but to picture what was here before.

District Six was home to a vibrant, close-knit, mixed-race community of working class people - mostly Cape coloured South Africans, but also Jews, Indians and the descendants of freed slaves - until the apartheid regime decided to reclassify it as a whites-only area, with the chirpy new name of Zonnebloem, meaning sunflower. PW Botha was Housing Minister at the time. In the interests, so he argued, of progress - slum clearance and urban renewal - the 60,000 residents were required to move out, and to separate, according to race. They were to make their homes in the townships beyond Table Mountain on the Cape Flats: blacks in Langa and Khayelitsha, coloureds in Mitchell's Plain. The four million residents who objected faced eviction by force. In 1966, the bulldozers rolled.

It's only now, nearly forty years on, that the former residents are trickling back very, very slowly. There's a neat terrace of brand new houses on the district's northern limit, home to the first families to resettle. Under the 1994 Land Restitution Act anyone who could prove their case could claim compensaton and the right to return, and the current government's target date for the resolution of all claims is 2005. But many of the displaced have said they will never go back - for them District Six is a place of ghosts, and the townships have become home. Some won't even set foot in Cape Town's flagship Waterfront development, final resting place of much of District Six's rubble.

It's hard to imagine the community as it used to be, but the District Six museum brings its spirit alive. Faithful to the spirit of reconciliation in modern South Africa, the museum makes no direct reference to the greed and stupidity of white minority rule, but the allusions are clear. Among the displays is one about pass cards, potent reminders of the restrictions imposed on individuals of certain racial groups. There's also a large black and white photo of Richmond Street before its destruction - shabby but bustling, just as Brian described it - plus snaps of District Six kids playing hopscotch and people hanging off the backs of trams. Dominating the space is a tower of old street signs, salvaged by one of the demolition team and hidden in his garden. Covering the floor is a large street map on which former residents have indicated where their houses used to be. As Brian points out his own family name, a party of school children come chattering in. "They're from Lavender Hill," says Brian, "a township named after a District Six street."

For many South African children, school trips are an unattainable privilege. Education for all is high on the agenda of the democratic government, but some children are excluded for heartbreakingly banal reasons. For the squatter camp kids, many of whom are the Xhosa-speaking sons and daughters of impoverished migrants from the Eastern Cape, language barriers can present major problems, as can the precise location of their nearest school - to a small child who has grown up in a rural area, crossing a highway can be too terrifying a prospect to contemplate.

It is with these thoughts in mind that our group files into the assembly hall of a school with a difference - the Chris Hani Independent School, founded and run by local volunteers to teach squatter camp kids. It's in Langa, Cape Town's oldest black township.

The strip-lit timber-shack hall is tiny, but compared to the classrooms, most of which once saw active service as shipping containers, it feels enormous. Filling well over half the space is the school choir - and they're raising the roof. Neatly uniformed, and ranging in age from seven to sixteen, they beam as they sing folk songs, spirituals and hymns and we clap enthusiastically at the end of each number.

At a signal from head teacher Maureen Jacobs, the choir segues neatly into Nkosi Sikilel ‘i Afrika. Who could fail to be moved by one hundred earnest young voices singing South Africa's unmistakably poignant national anthem? Blinking hard, I gulp back my emotions, and I know, without looking round, that my companions are doing just the same. Like devoted parishioners at the end of a particularly fine organ voluntary, we all drop something in the collection box. But later, when we're all back in the minibus, one of the New Zealanders speaks out. "I'm really not sure what I'm feeling right now," she says, before our guide clambers back in. "It must be so disruptive for those kids to have tourists trooping in and out of their classes every single day. Are we really giving them the right message, by having them receive us like that?"

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It's the first expression of discomfort since Brian drove us into Langa to introduce us to 21st century township life. He warned us not to wince as we drove past women barbecuing sheep heads (called "smilies") or sorting through offal at stalls on street corners. He pointed out the hostels where working males used to live in inhumanly cramped conditions for most of the year. He also showed us the area in which, a few months before, 900 shacks burned down in an afternoon, leaving eight people dead. But our stop at the school has been our first opportunity to step out of the minibus and become participants, rather than passive observers. The New Zealander's comments are enough to break the reverent silence in which we shuffled out of the assembly room, and we wonder to each other whether, for all our good intentions about joining the tour to connect with the real South Africa, we've ended up on a "human safari" after all.

Brian rejoins us and we continue the tour. "We call this neighbourhood Langa's Beverly Hills," he says as we cruise through a quiet and relatively well-to-do area. It's home, he tells us, to black professionals - doctors, teachers and civil servants - who have chosen to remain in the townships even though they could probably afford to move elsewhere. Here, then, are the positive role models that Langa's children need so badly. But the burglar alarms, fences, window bars and security gates that distinguish their homes speak as loudly of paranoia as of success.

On the way to our next stop we drive past Guguletu cemetery, where fresh graves bear testament to a bitter fact of life in the townships - it's thought that as many as eight out of ten residents may be HIV positive. Burials tend to take place at weekends, to enable the relatives of the dead to travel to Cape Town from the homelands. "On a Saturday, this place is as busy as a marketplace," says Brian.

He takes us to Khayelitsha, a black township which has mushroomed since 1984 and which now measures over 5km from end to end. Designed as a workers' dormitory, rather than a self-contained community, the township still has no apparent focus - no central shopping area or meeting place. It's home to 1.2 million people, of which more than two thirds are officially unemployed; few of those in work earn more than the minimum wage of around £80 per month. As we enter, we drive past a sign saying You are now entering an urban renewal area, followed by a derelict Caltex petrol station, closed in the face of persistent crime.

We're allowed off the minibus for a second time on a narrow, dusty street of small cement-block and timber houses, and are introduced to Rosie Gwadiso, the founder of a community kitchen which provides nutritious meals for local children who would otherwise go to school hungry. The distinctive smell of township cooking hangs in the air. Rosie invites us in.

Having moved from the Transkei into a Cape Flats shack, Rosie now lives in a small "Mandela house" built with a subsidy provided by the government's re-housing programme. The modest luxuries in her living room - a television, a stereo and a three piece suite - are all gifts from foreign visitors bowled over by her selfless commitment to those less fortunate than herself. As well as feeding the neighbourhood kids, she runs HIV/AIDS awareness classes. "I lost my sister to AIDS," she says, "so, I cannot just fold my arms and do nothing."

We leave Rosie's place feeling inspired by one woman's determination to make a difference, and head across the township to the tiny empire of another very determined woman. Vicky Ntozini is the owner, architect, designer, housekeeper and head chef of Cape Town's original township bed and breakfast, known as Vicky's B&B. We're ushered into the living room of her timber and corrugated iron shack and are encouraged to inspect her two guest rooms. But there's something about the way she rattles off a pre-prepared welcome speech that suggests that she's been in this business too long to have any real interest in yet another bunch of culture-shocked white tourists. Chatting to her later over a lunch of mealie pap and spicy sausages, her jaded look changes to a spark of relish as she tells me about her expansion plans - she wants to add a second storey with more guest rooms. It's clear that what started as a simple mission to share a cultural experience has turned into quite an exciting business prospect.

Back in the city centre, my hotel's abundant comforts leave me feeling slightly uncomfortable inside. My perception of Cape Town's rich-poor divide has shifted - the city is much more multi-layered than I realised.

Over a glass of local Shiraz with a Capetonian friend, I ask why it is that so few white South Africans take township tours. She tells me that it's hard for locals to shake the memory of the townships being no-go areas for whites. Some people are still scared by the idea of them, stirred up by stories of drug addiction and gangland crime, and those that aren't simply have no desire to confront the realities that the townships present in black and white. "Apartheid, and the state of mind it bred, was a religion," she says. "It's off the statute books, but we still need to conquer it fully in our minds."

"Plus," she adds, "the people running these tours know that for tourists they're something foreign and adventurous. If somebody were to start running tours of London's poorest council estates, would you book?" I have to admit I'm not sure. But I still want to see more of the Cape Flats.

The next day, instead of joining another minibus tour, I decide to set my own agenda, and hire a guide to drive me back to Khayelitsha. It's early, but for the working locals the day started before light, with a breakfast of bread and peanut butter or home-made tomato relish, followed by a cramped minibus journey into town or out to the winelands. The streets are empty apart from the shopkeepers and stall holders, and a few groups of unemployed men sitting on upturned crates, chewing the fat.

I've asked to visit Golden Nongawuza, the township artist who makes flowers out of tin cans, and manages to support a family of six on the proceeds. We walk through an impeccably swept compound to his studio, a lean-to tacked onto the side of his small house. Piled under a workbench are his raw materials - fizzy drinks cans - and blossoming all around are bunches and bowls of the jaunty metal flowers that I've already seen in a few Cape Town gift shops. Keen to show me how it's done, Golden selects a Red Bull can from the pile, and sets about cutting and shaping the metal. Within minutes, he's holding up a blue and white flower with a reticent smile. As I'm not with a group, there are no or pre-rehearsed speeches or recitations, and I feel under no pressure to buy anything - but of course I do.

To find out more about Khayelitsha's burgeoning community crafts scene, we drive over to the Khayelitsha Craft Market near Lookout Hill, stopping every so often to chat to a few more participants in the local enterprise culture - barbers, fruit sellers and phone booth managers running their businesses out of brightly painted shacks or shipping containers. At the craft market, we're greeted by marimba music, and one of the craftworkers shows me her latest project - a beaded mobile phone cover. She tells me that the market receives regular visits from people on travelling with a township tour or independently with their own guide. "Business is good, it's growing by word of mouth," she says. Run as a cooperative, the market provides women with training and materials and offers them a stall from which to sell their crafts.

After browsing table after table of pots, necklaces and recycled crafts I'm ready for a drink and we head for a nearby shebeen. Inside, the barman hands us cold beers through the wire grill that blocks off the bar, and we settle down to watch a spirited game of pool while jazz plays in the background. We're soon cajoled into joining in - our new friends tell us with a grin that there's no such thing as a spectator sport in these parts.

At the end of the day I check into my accommodation for the night - a room at Khayelitsha's Kopanong B&B. It's been recommended to me several times, and I can see why - there's a homely feel to this tidy bungalow decorated with African fabrics and Golden's unmistakable flowers. I'm welcomed in like a long-lost friend. A distinct chill descends over the Cape Flats after dark but once I've piled on a few extra blankets and curled myself up in a cocoon I feel every bit as comfortable as I had in my smart hotel.

Kopanong, which means "meeting place", is run by Thope Lekau, who used to be a rural development worker, empowering women to cope with the challenges that are a fact of life in South Africa's poorest communities. As the eldest of seven children, Thope learned how to look after people at a very early age, and developed a flair for catering that she's passed on to her daughter. In the morning, at a table groaning with the huge breakfast the two of them have prepared (fruit, eggs, sausages, tomato relish and steamed bread) she explains that the sense of acute segregation in South African society is slowly beginning to ease.

"Before, the only white people you'd see round here would be policemen - on their way to arrest somebody," she tells me. "But now, people come from all over the world. My neighbours love to see all the cars rolling up - they're impressed, and they feel proud!

"With so many foreign visitors coming into the townships, I'm optimistic that white South Africans might follow soon, and that'll be a real indicator of change. The big hope is that in ten years' time, there'll be no more township tours - not because people have lost interest, but because there'll be no more townships."

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With thanks to South African Airways (www.flysaa.com), the Cape Grace Hotel (www.capegrace.com), the District Six Museum (www.districtsix.co.za) and Grassroute Tours (www.grassroutetours.co.za). For details of Kopanong and other township B&B's, turn to our guide on page 102.