"Can we deny that Cape Town is still the most racist city in South Africa?" asks Kenneth Lukuko, in an essay contained in the SA reconciliation barometer survey (pdf) published on Thursday. "Perhaps we can't."

During Nelson Mandela's presidency, he notes, "it was the only city in which he was met with a placard that referred to him with the K-word [the taboo term "kaffir"]. And it has taken Cape Town longer than anywhere else in the country to name a major public space or amenity after Mandela, although it is the city associated most closely with his incarceration, as well as being the backdrop for scenes of his release, which were broadcast all over the world."

But while Cape Town is regularly accused of being a neo-apartheid stronghold the annual survey by the Institute for Justice and Reconciliation (IJR) raises some difficult questions about the rainbow nation project as a whole.

Eighteen years after the end of white minority rule, it found, 43.5% of South Africans rarely or never speak to someone of another race. Little more than a quarter (27.4%) interact with a person of another race always or often on ordinary weekdays, while 25.9% do so sometimes.

Less than one in five (17.8%) South Africans always or often socialise with people of other races in their homes or in the homes of friends. A further 21.6% do so sometimes, and more than half (56.6%) rarely or never socialise across race lines.

The survey has been conducted every year since 2003. Whereas both contact and socialisation levels increased during the early years, little has changed since 2010. "Certainly, latent and overt stereotypes, fear or trepidation about others, and even naked racism may have contributed to static levels of interaction and the slow pace at which social bonds are being forged between South Africans of different race groups," the report notes.

"Indeed, in 2012, 41.4% agree that they find the 'ways and customs' of people of other race groups difficult to understand. However, each year the reconciliation barometer survey also finds an almost entirely linear relationship between contact, socialisation and living standards: South Africans who live in affluent households in urban areas interact and socialise the most across racial lines, and those in the least affluent households – often in rural areas, homogenous former townships and informal settlements, and where formal sector employment is low – interact and socialise the least."

The poll found that 61.8% of South Africans believe that national unity across historical divides is desirable, although agreement is lower among white (49.4%) and coloured (mixed race) (50.5%) youth, who display higher levels of ambivalence – and 59% believe that this is possible.

Disapproval of racial integration in schools, residential neighbourhoods, workplaces and marriage has continued to decline overall. But still 18.1% of South Africans say they would not approve of living in a residential area in which half their neighbours were people of other races, and 20.3% would disapprove of working for and taking instructions from someone of another race.

There are now nearly 20 million South Africans with no experience of living under apartheid, a demographic trend that the party of liberation, the African National Congress (ANC), will have to contend with. The survey found that a clear majority (83.8%) agree that apartheid was a crime against humanity and 82.5% agree that before the transition to democracy, the state was responsible for committing atrocities against anti-apartheid activists. A further 81.1% agree that the apartheid government wrongly oppressed the majority of South Africans.

Yet differences again emerge along racial lines, with recorded agreement lower (68%) among white South Africans than other groups (74%). A split is evident in response to a question that assesses apartheid's economic legacy: whether or not black South Africans are still poor today as a result of the lasting effects of apartheid.

The poll found 82% of black South Africans agree that this is the case, as do 73.3% of Indian/Asian and 61.4% of coloured South Africans. Only about half (50.6%) of whites agree.

White, coloured and black youth are all more likely than adults to question whether apartheid was a crime against humanity and that the state committed atrocities against activists: 27.7% and 24.6% of white youth agree that these statements are certainly or probably not true.

Higher percentages of white (38.0%), Indian/Asian (28.4%) and coloured (32.2%) youth than adults feel it is untrue that black South Africans are poor today as a result of apartheid's legacy.

The report warns: "These findings pose difficult questions about how young people understand South African history, their sources of information, and whether a struggling school system has missed an important opportunity for education on the past, civic identity and citizenship, and national and constitutional values."

The IJR said its Reconciliation Barometer survey was conducted through face-to- face interviews with a nationwide sample of 3,565 South Africans representative of the adult population, with an equal gender split.