David Lammy's frustration over his inability to influence events at London Metropolitan University led him to contrast the case with the "Baby P" affair, Times Higher Education can reveal.
The higher education minister's comments appear in heavily redacted correspondence released by the Department for Business, Innovation and Skills following a Freedom of Information Act request.
They date from June 2009, at the height of the dispute between London Met and the Higher Education Funding Council for England over responsibility for inaccuracies in the university's student-data returns.
London Met had declared a student non-completion rate of about 3 per cent for several years, while Hefce put the figure at 30 per cent.
The correspondence, revealed in our cover feature this week, highlights Mr Lammy's growing frustration with London Met management's lack of accountability and legal constraints on his ability to intervene.
A memo from Andrew Battarbee, deputy director of higher education shape and structure at BIS, to Martin Williams, head of its higher education directorate, says: "David understands the legal position but he contrasted this with the Baby P case sackings."
He was referring to the removal from post of Sharon Shoesmith, head of children's services at Haringey Council, by Ed Balls, secretary of state for children, schools and families, in December 2008 after the death of 17-month-old Peter Connelly.
This month, lawyers for Ms Shoesmith, who was later sacked, claimed Mr Balls and the Department for Children, Schools and Families had applied pressure on Ofsted inspectors to amend a report into the case.
Other correspondence on the London Met affair reveals Mr Lammy's desire for an independent review of the crisis and his conviction that the university's own review would not uncover the full facts.
A memo sent by Mr Battarbee in July 2009 shows that the minister was preparing to announce that he would ask an independent figure to investigate.
"He mentioned - it seemed to come from thin air - Brenda Gourley (former vice-chancellor of The Open University) as someone who might do this," Mr Battarbee writes.
He adds that setting up a separate review would be "difficult", partly because it was unclear how London Met's governors would react.
"We know from the 2008 process and the threats to sue for defamation that some governors will readily retreat to the bunker and start opening fire," he writes.
The civil servants later convinced the minister that he had no mechanism to set up a separate inquiry under which the cooperation of all parties could be guaranteed.
Mr Lammy's fears were not realised, as the two reviews commissioned by London Met - from Sir David Melville and KPMG - were highly critical of the university's management and governance.
London Met's lay governors and vice-chancellor Brian Roper resigned in 2009. Two senior managers - finance director Pam Nelson and deputy vice-chancellor Bob Aylett - are currently under investigation.