Minister for Education Mary Hanafin has backed an independent investigation into alleged financial mismanagement and bullying of staff at UCC.
While the decision to appoint an examiner is firstly one for the Higher Education Authority (HEA), the Minister said she favoured such a move as the continuing controversy was not good for the college.
"It is not in the best interests of the university for this to keep rolling. In light of all the Government investment I need confidence in the system, and anything that is going to interfere with this needs to be dealt with."
The HEA is due to meet the governing authority of UCC and its president, Prof Gerry Wrixon, next week to examine allegations made by senior staff.
Last week former UCC president Prof Michael Mortell backed calls by a senior member of staff, Prof Des Clarke, for an inquiry at the college.
Ms Hanafin said the allegations against Prof Wrixon had already been dismissed by the HEA. "They were aired and knocked on the head a few years ago but there are eminent people on both sides - including people of status like Prof Wrixon and Prof Mortell - so we need to clear it up."
The Minister said while the allegations were "about Gerry Wrixon they were also about finances and about the spending of money on buildings. Therefore it could be very easy to clear up."
The Minister's backing for an investigation represents a setback for Prof Wrixon, who is due to retire from his post in January. Two years ago a HEA inquiry largely vindicated Prof Wrixon's management of the university; he is likely to see any new investigation as unnecessary.
Prof Wrixon has accused his critics within the college of running a personalised campaign against him. For their part, Prof Clarke and other critics accuse Prof Wrixon of a confrontational management style.
In recent years UCC's debt has spiralled to almost €40 million, although some believe it could even be more. Attention has also focused on its decision to proceed with a new IT building for which funding has still to be approved by the department.
Ms Hanafin pointed to the huge level of Government investment in third-level education, including the new €300 million Strategic Innovation Fund. She said given this investment we do not want a situation where there was tension at any college.
Prof Wrixon is one of the most contentious figures in Irish education. He has been praised by former tánaiste Mary Harney for his visionary and pro-business approach. In Government he and UCD president Dr Hugh Brady are credited with the "modernisation" of third-level education which has seen extensive restructuring and a new stress on scientific research.
However, Prof Wrixon has had a series of legal and other battles with senior staff and members of the academic council at the college. Last year over a dozen academics were openly critical of his management style on RTÉ news.
Despite this, the Government approved a special extension of service for him beyond his normal retirement age. However shortly after Prof Wrixon surprised his critics and the Government when he announced his intention of stepping down in January.
Prof Clarke had asked the Government to appoint a visitor, up to the level of a High Court judge, to examine the UCC controversy. However Ms Hanafin said such an appointment would be taking the allegations too seriously.
The independent inquiry is unlikely to ease the controversy surrounding UCC. Already, critics of Prof Wrixon have signalled concerns about the appointment process now under way to find his successor.