The admission came as the university set up an equal opportunities committee and welcomed a report recommending 93 improvements in its procedures.
The pro-chancellor, a Catholic businessman, John McGuckian, said candidly: 'There absolutely was discrimination in Queen's University. It is beyond question and a matter of public record that when the current bursar took up his position there was no Catholic employed, and there never, ever had been a Catholic employed, in the bursar's office.'
He added: 'It is accepted that there was discrimination in Northern Ireland. Queen's was one of the major institutions, and it is a fact that institutionally there was discrimination. It was endemic in the structure of the society.
'There are something like 14,000 people involved in Queen's, between students and staff and administrators.
'I'm not going to sit here and say that they're 14,000 saints. You can make up your mind how many bad guys there were - we're not saints in here, but we're trying to do our absolute best to make sure we behave ourselves.'
The vice-chancellor, Dr Gordon Beveridge, was more defensive in his presentation. He said: 'No, I don't accept there is discrimination at Queen's. 'If you mean discrimination by individuals, of course legally discrimination can arise because procedures aren't adhered to, but that doesn't necessarily mean that people have discrimination in their heart.' He did not believe recent criticisms had undermined his position.
Mr McGuckian said he now thought there was a serious commitment to make the university a model for the community, and he hoped this would be achieved quickly. He pointed out that the percentage of Catholics employed had risen from 21 per cent to 28 per cent in recent years.
The report by fair employment experts was yesterday accepted unanimously by the university senate, which accepted virtually all of its 93 main recommendations.
These include incorporating a commitment to equality in the university's statutes, increasing the number of Catholics and women on the senate and committees, and changes in recruitment and promotion procedures.