Many young people have grown up with division
The research, conducted among 4,800 households in a dozen estates across the city suggests the divisions between Catholics and Protestants are even greater and that inter-community violence is on the increase.
Young people are particularly highlighted as fostering the air of division, with as many as 68% saying they "have never had a meaningful conversation" with those of the other religion.
Will Glendinning, chief executive of the Community Relations Council, believes the survey is a true reflection of the situation, and that decision-makers must work round the divides.
'Self-imposed apartheid '
He told BBC News Online: "As far as young people are concerned, if you've grown up in an area of strong segregation it is not surprising that you do not speak to those on the other side.
"People have mental maps of where it is safe to go and where it is not safe to go."
Policy-makers must accept community division as a key part of regeneration and town planning issues, Mr Glendinning added.
"If not, these issues will be left to drift and we will have a self-imposed system of apartheid here," he warned.
The report's author Dr Peter Shirlow is presenting his findings to the Royal Geographical Society and Institute of British Geographers conference in Belfast on Saturday.
A senior lecturer at the University of Ulster, he said the research contradicts what politicians involved in the peace process hoped was happening in Northern Ireland.
He said: "Where is the agenda to create mutual spaces, where is the agenda to create meaningful community contact?
"These things are not happening, so although the peace process may be working in certain places, it is also failing in others and quite miserably in certain cases."
Poor relations
The research was carried out among areas of inter-faith population, divided by the so-called "peace lines".
The survey showed 62% of those questioned felt community relations had worsened since 1994, after the first ceasefire.
Only 22% would be happy to go shopping in areas dominated by another religion and 72% of all age groups questioned refused to use health centres in areas where the population was mainly the other religion.
There were signs of accord in rural and suburban areas where people of mixed religion are found to be mixing more than 1994.
Mr Glendinning said areas of division must be recognised in Northern Ireland's towns and cities, without them being allowed to aggravate disagreement, resulting in violence.
"The first way a place becomes marked out is by the use of sectarian symbols, such as flags, murals and pavement markings.
'Challenge'
"As an organisation we work to tie this in with regeneration so that people can still display a cultural identity."
He said there had been the beginnings of a change in policy, to accept that neutral spaces in different communities are needed.
"That outcome has not been worked on and that is what is needed.
"The challenge to our communities is not to forgive and forget - otherwise problems just reappear - but to remember and change, to recognise what has happened and shift."
The Community Relations Council will be looking at the university research findings at a seminar in Belfast on Monday, among an audience including senior policy makers in Northern Ireland.