Despite calls by Scottish ministers for restraint, documents released under Freedom of Information legislation show 14 university principals and vice-chancellors in Scotland received more than 3 million in the 2009-10 financial year.
The packages for the heads of the institutions, which received around half of their funds from the taxpayer, included more than 2.7m in basic salaries and more than 300,000 in pension contributions and other payments.
The total figure is almost certainly an underestimate, as Aberdeen University, which has recently parted company with its principal, did not supply details of his successor's package.
Heriot-Watt and Napier universities in Edinburgh also declined to provide details.
The documents show nearly all university chiefs were paid more than Prime Minister David Cameron, on 142,500, and Scotland's First Minister Alex Salmond, on 82,094.
The continuing high salary packages will increase pressure for university pay to be brought under the scrutiny of the public spending watchdog, the Audit Commission.
Labour peer Lord Foulkes, who will raise the issue with education secretary Michael Russell on Thursday at Holyrood, said: "It's very worrying that universities are not democratically accountable in the way that the majority of the public sector is."
Last year, Anton Muscatelli, the principal of the University of Glasgow, was Scotland's joint top-earning university boss with a salary of 250,000. Although he accepted a pay freeze from the previous year, additional payments totalled 40,000 – up more than 5,000.
His salary was matched by Professor Jim McDonald of the University of Strathclyde, who was paid 250,000 in salary – up 18,000 on the previous year – and 40,000 in extras.
Bernard King, the principal and vice chancellor of Dundee's University of Abertay, was awarded 222,000 in basic pay and 33,000 in top-ups. The University of the West of Scotland's principal and vice chancellor Professor Seamus McDaid received more than 212,000 in salary and more than 31,000 in extras.
The University of Stirling's principal and vice-chancellor Gerry McCormac was paid 215,000 in salary, an increase of 1,000, and more than 34,000 in extra cash – up 4,000 on the previous year.
Those taking decreases included Dundee University's principal and vice chancellor Sir Alan Langlands, who received a salary of 211,000 (down more than 4,000) and 33,000 in additional payments (down 3,000).
Edinburgh University said its principal, Sir Timothy O'Shea, who was paid 230,000 in 2009/10, declined a pay rise and increase in bonuses in January this year. But Foulkes said: "These figures show that a huge chunk of public money that goes into higher education is being used to pay the top people at universities."
The salary packages come against the background of budget cuts at many universities. Heriot-Watt University has announced negotiations on compulsory redundancies, while Napier University has proposed more than 100 job losses. Tutors at St Andrews University are also facing redundancy.
But Alastair Sim, director of Universities Scotland, said: "Every penny universities get and spend is subject to internal audit by the university court, independent external audit and audit overview by the Scottish Funding Council."
A Scottish Government spokesman said that as universities accepted taxpayers' cash, their spending had to come under increasing scrutiny.