The data, pulled together by the Reform Scotland think tank, also shows that 19 public-sector chief executives earn at least as much as the First Minister - with 15 of those in wage bands that would put their earnings above Alex Salmond's.
Alison Payne, the organisation's research director, said the revelations made the case for greater transparency across the public sector. The Scottish Government hands over to quangos around one-third of its annual budget, which covers sectors such as health, sport and enterprise.
The vast number of arms-length bodies in Scotland, ultimately accountable to ministers, continues to fuel a debate about democratic accountability.
Reform Scotland, which has championed market-based solutions in the public sector, has now produced a bulletin containing quango CEO salaries.
The top chief executive earners in 2011-12 include Richard Ackroyd of Scottish Water, who died suddenly in 2012 and was replaced by Douglas Millican, Lena Wilson of Scottish Enterprise and James Barbour of NHS Lothian, who retired in 2012 and was replaced by Tim Davison. They respectively earned up to £240,000, £205,000 and £195,000.
Others in the top tier include Robert Calderwood, the boss of NHS Greater Glasgow and Clyde and Barry White, chief executive of the Scottish Futures Trust, who earned up to £190,000 and £185,000, respectively, in the same year.
The higher end of the pay range for these five CEOs, as well as 14 others, was more than the £140,647 salary received by the First Minister. However, the First Minister also has the grace-and-favour Bute House and a chauffeur-driven car at his disposal.
A larger number of CEOs - 39 - were able to take home more than the £100,748 payable to Cabinet secretaries.
This bracket includes the chief executives of 10 health boards, the Scottish Legal Aid Board and various culture bodies.
Payne said: "It may well be the case that the salary for a particular chief executive is justified - although it is difficult to argue that any public-sector salary should be higher than that of the person running Scotland, the First Minister. However, the key problem is the use of quangos, which are neither fully democratically accountable nor fully independent of government, leading to a lack of transparency and accountability over their activities, including the level of salaries paid."
The research was welcomed yesterday by Scottish Conservative chief whip John Lamont, who said: "The SNP promised a bonfire of quangos, and that simply hasn't happened. If there were fewer of these organisations paying top dollar for talented people it would not be as big an issue.
"As it stands, that justification isn't taking place, which angers the public and leaves an impression that their money is being wasted."
A Scottish Government spokeswoman said: "Public bodies are accountable to Scottish ministers and are ultimately accountable to the Scottish Parliament. The salaries of public-sector staff are set in accordance with the Government's pay policy, which has been subject to significant restraint in recent years and for which ministers are also accountable to Parliament.
"Since October 2007, the number of devolved public bodies has reduced from 199 to 113, exceeding the Government's original target to reduce the number of devolved public bodies by 25%. Mergers alone have saved £78 million between 2007 and 2012-13, and further savings will be delivered on a recurring basis."