Universities are facing funding cuts
More than 80 heads of universities earn more than the prime minister and some have seen their pay treble in the past decade, a Guardian report says.
The probe said 19 vice-chancellors earned more than £300,000, with the top earner netting £474,000.
The report comes as England's universities face funding cuts of £215m next year, with further hardship ahead.
Universities UK (UUK) said pay was in line with heads of similar bodies and that rises were reducing this year.
The Guardian figures suggest some vice-chancellors got pay rises of as much as 15 or 20% in 2008-9.
But both the universities umbrella body UUK and the Universities and Colleges Employers' Association (UCEA) said these pay decisions would have been taken in a very different financial climate.
They were also not calculated over like-for-like pay periods, they said.
Universities UK chief executive Nicola Dandridge said: "The figures relate to pay in 2008-09 which will have been agreed by independent remuneration committees at that time.
"The sector's own research into the remuneration of vice-chancellors and principals in 2008-09 shows the median increase was 8.9% which is in line with the overall staff pay rises for that same time period.
"We are now in quite a different funding climate and the results of our survey of vice-chancellors and principals' salaries for this year (2009-10) reflect this.
"For this period (2009-10), the average increase is 0.5% with 70% of vice-chancellors and principals receiving uplifts of 0% or 0.5%."
The UCEA said: "Feedback from institutions where the outcome of 2009/10 pay reviews have been finalised show that 70% of heads of institutions are either receiving no increase at all or 0.5%.
"Institutions are facing extremely tight budgets and financial constraints and recent announcements of cuts to sector funding suggest that this is a trend that will continue."
But general secretary of the University and College Union Sally Hunt said the pay rises senior staff had enjoyed in recent years had been "a constant source of ridicule".
The highest paid vice-chancellor is Professor Sir Andrew Likierman, of London Business School, who is said to earn £474,000.
A statement from the school said it competed in a global market to attract the best business and management thinkers.
It added it was ranked first in the world for its full-time MBA.
One of the highest paid vice-chancellors is at Oxford University with a reported salary of £327,000.
The university defended the salary saying it was the number one university in the country and the biggest research provider.
A spokesman said: "The published salary applies to the final year of Dr John Hood's vice-chancellorship.
"External research income to the university doubled over the five years of his vice-chancellorship and in those five years a fundraising campaign began and raised £770m."
The salary of the current vice-chancellor Professor Andrew Hamilton would be published in the financial accounts at the end of 2010.