Academics and student leaders called for new legislation to restrict pay for senior managers in the sector after an average increase of more than 4% in 2012/13 at a time when staff are taking industrial action over a pay offer of 1%.
The figures show the largest increase was a 24% rise for Professor Steve Chapman from Heriot-Watt University, Edinburgh.
Mr Chapman accepted a £20,000 increase in his basic pay and a £20,000 bonus in 2012/13 to bring his overall salary package, excluding pensions contributions, to £210,000.
The second highest increase was the 11% awarded to Professor Dame Joan Stringer, the outgoing principal of Edinburgh Napier University, in her final year in post.
Professor Seamus McDaid, the out-going principal of West of Scotland University, which has its headquarters in Paisley, took an 8% pay rise in his last year, bringing his salary to £235,000.
Professor Gerry McCormac, principal of Stirling University, was awarded a 6% increase, taking his salary to £205,000, although a spokesman said he had donated the extra money to a fund to help students.
The highest-paid principal in Scotland is now Professor Sir Jim McDonald from Strathclyde University, who accepted an increase of 5% in 2012/13, bringing his salary to £262,500.
However, many other principals showed restraint over pay, with some accepting nothing and others taking an increase of about 1%.
The salaries dwarf those earned by senior UK politicians, with Prime Minister David Cameron paid £142,000 and Scotland's First Minister Alex Salmond entitled to £140,000.
The rises are particularly galling for unions representing academics, who are being told money is too tight to offer them more than 1%. In addition, there has been a concerted drive in Scotland in recent years to obtain more clarity and accountability over the salaries of university principals which has been resisted by institutions.
In 2012, a review of university governance chaired by Professor Ferdinand von Prondzynski, principal of Robert Gordon University in Aberdeen, called for a number of changes, including the abolition of bonuses.
It also called for university remuneration committees that set the pay of principals to include members of staff and students to increase transparency. However, a new code of governance published by a steering group of experts chaired by Lord Smith of Kelvin later dismissed the suggestion, arguing principals' pay should continue to be decided by the current remuneration set-up.
Mary Senior, Scottish official for the University and College Union, said: "The hypocrisy of principals taking pay rises of up to 24% last year will not be lost on staff working in universities.
"These are the same university principals who have talked down to their staff and told them to accept a 1% increase - representing yet another real-terms pay cut - as it is the best they can expect.
"What is acutely embarrassing for the sector is the complete lack of self-awareness from principals over their pay rises, and their continued greed underlines the urgent need for greater scrutiny of pay and a role for staff and students on remuneration committees."
Gordon Maloney, president of NUS Scotland, said: "At a time when staff are striking over a 1% pay increase, everyone will be rightly wondering how principals can justify pay increases and bonuses of up to 24%.
"It would be completely out of touch for university principals to think we didn't need to have greater controls on such high levels of pay. If universities can't provide a solution then we need to look to government and funding bodies to consider further legislation."
A spokeswoman for Universities Scotland, which represents principals, said: "Of course we expect principals' salaries to come under intense scrutiny, but it's important to give the figures some context. Many principals have taken a below-inflation increase over the last year. In instances where the increase is higher, we're aware of at least one case where an uplift was agreed following many years in which the principal in question refused to take an increase.
"Universities are highly efficient users of public funding and receive more than half of their funding from private sources. Principals are in charge of multi-million-pound enterprises and responsible for many thousands of staff and students and hundreds of stakeholders. It is a complex and demanding job which commands a high salary."
A spokesman for Heriot-Watt said: "The university is performing exceptionally well and is led by an outstanding principal who remains at the lower end of the principal pay rates for comparable universities.
"The remuneration is reviewed annually and has been in the lower decile of its peers since Professor Chapman took up the post in 2009. In 2012/13 the principal's salary reflected the outstanding successes of the university."