Universities Minister Jo Johnson says that excessive pay for university bosses will be brought "under control" by new regulations, which he told the BBC would appear in the new year.
Mr Johnson said he was "absolutely convinced" a new regulator, the Office for Students, will tackle pay concerns.
The minister promised "greater restraint... in setting top salaries".
It comes after protests over the former head of Bath Spa University receiving more than £800,000 in her final year.
'Has there been a problem? Most definitely'
Mr Johnson's comments follow a series of protests over vice-chancellors' pay in recent weeks - including at the University of Bath, the University of Southampton and this week at Bath Spa.
"Has there been a problem? Most definitely," said Mr Johnson. But he said universities now recognised the need to answer public concerns about value for money.
"I think they really are starting to get it," said the universities minister, who said that a "new regulatory framework" would be published by the government in the new year.
Mr Johnson said the Office for Students would require universities to ensure their "governance is fit for purpose".
Universities are autonomous institutions, but the minister said there needed to be an understanding of the "perception of value for money" from the public.
In the new year, this would mean rules requiring much clearer evidence of the independence of committees deciding vice-chancellors' pay.
Universities will also have to explain the pay gap between top earners and the rest of their staff.
"When students are paying for their own tuition fees, there is a greater expectation of greater accountability to students, but also to the taxpayer, who is underwriting the student loan book," said Mr Johnson.
"Value for money is at the heart of why we set up the Office for Students," he said.
But he said he was "concerned that the proportion of students in England who feel they are not getting value for money is greater than those who feel they are getting good value for money".
The universities minister said that details of the "major review" of tuition fees and university funding - promised by Prime Minister Theresa May - would also appear in the "coming weeks".
But Mr Johnson has defended the structure of the current system as ensuring that more disadvantaged students can go into higher education and that universities are better funded.
Sally Hunt, leader of the UCU lecturers' union, welcomed Mr Johnson's assurances on pay, but warned that he could become "the latest in a long line of ministers to have seen previous calls for pay restraint ignored".
"Put simply, the status quo cannot continue."
In the dispute over pay at Bath Spa University, there have been calls by the UCU lecturers' union for an "urgent overhaul" of senior university pay.
Accounts for Bath Spa University show Prof Christina Slade was paid £429,000 "for loss of office" on top of her £250,000 salary and other benefits.
A spokeswoman for Bath Spa said the sum represented "value for money".