Irish universities need to be much more accountable to students and taxpayers, according to Prof Skilbeck.
Prospective students, he said, should have access to all assessments conducted on various university faculties and departments. These assessments by independent experts should be widely available to the media and to the public.
Prof Skilbeck, who has received an honorary NUI doctorate for his services to Irish education, defended his recent report for the Higher Education Authority. It called for a radical overhaul of the Irish university sector in which colleges built stronger links with industry and the wider community.
In an interview, he confessed to being greatly amused by charges that he was promoting a "Thatcherite" agenda and undermining the traditional intellectual freedom of colleges. He said a culture of secrecy and defensiveness had built up in colleges but the question had to be faced - who are the universities responsible to?
It was possible, he said, to respect the tradition of free intellectual thought while making a case for colleges to be more responsive to the needs of society - and more accountable to the taxpayer.
In his address to a North-South higher education conference in Armagh, he also said universities in Ireland have a "moral responsibility" to show leadership in cross-Border dialogue and to see co-operation "not as incidental, but as one of their primary responsibilities".
The two-day conference is being attended by the heads of seven of the nine universities on the island of Ireland.
Prof Skilbeck, an Australian, is a former deputy director for education at the OECD. He is the author of a number of influential international reports on higher education.
He told the conference Irish universities would "have to become more entrepreneurial" and universities in the Republic "will be increasingly subjected to the rigours of appraisal and public accountability".
Other key conference speakers included the former US Education Secretary in the Clinton administration, Mr Richard Riley, and the Director-General of Education and Culture in the European Commission, Mr Nikolaus van der Pas.
The conference, titled "Ireland as a Centre of Excellence in Third Level Education", has been organised for the Department for Employment and Learning (Belfast) and the Department of Education and Science (Dublin) by the Centre for Cross Border Studies.