The allowances, which flout national pay policy, came to light in last week's review body report on top publicsector pay, which was highly critical of the arrangements.

It ordered a pay freeze for the presidents involved until the allowances are withdrawn. The review body did not name specific colleges but the Sunday Tribune has established that the presidents of at least two universities received unauthorised allowances. The top-up allowances mean some university presidents "are being paid more than we believed to be justified", the body said.

UCD confirmed its president, Hugh Brady, has received an unauthorised annual allowance of 12,000. "Our understanding is that this allowance is to be subsumed within the increase recommended by the review body, " a spokesperson said. However, such a move would put UCD on a collision course with the government review body which warned that unauthorised allowances must be "withdrawn" before pay increases are approved.

A UCG spokesperson said its president, Iognaid O Muircheartaigh, is not currently in receipt of any allowance but the spokesperson was unavailable to comment on unauthorised allowances since 2001. The review body recommended the UCD president receive a 19% increase, bringing his official salary to 270,000. The UCG president is to enjoy the same 270,000 . . . a 30% increase.

Officials at education minister Mary Hanafin's department are known to have raised concerns about other perks to senior university staff, including company cars, bonus schemes and contributions to personal assurance plans. None of these benefits are permitted under national pay rules. The review body report stated the recommended salaries for university heads "represent the total remuneration for the posts concerned and no additional payments should be made".

Several universities, and the Higher Education Authority, now face scrutiny about who authorised the payments.

"We fail to understand how this situation can occur since payments of this sort require the approval of the minister for education and the minister for finance, " the body stated.

The Sunday Tribune has also learned that several academics in one third-level institution are receiving remuneration packages which include salaries above 240,000, pension contributions up to 40% of income and annual bonus payments. Under the Education Act, universities are legally obliged to stick to national pay policy. Government approval is necessary for exemptions in exceptional cases, generally to recruit academics with an international profile who earn a higher income abroad.

In response to queries last week, the TCD provost and the DCU president confirmed they had not received any top-up allowances. "I have not been in receipt of any payment or allowance over and above the review body's decisions, either now or at any time since I became president of DCU, " Ferdinand von Prondzynski said. The UL president was unavailable while UCC failed to respond to the query.