Reform Scotland highlighted the difference in pay as part of a call to curb bumper salaries and make the system more transparent. A report by the group is based on details for 58 of 72 quangos in Scotland.
It shows 39 earn more than a cabinet secretary and 19 earn as much as First Minister Alex Salmond, who is on just in excess of £140,000.
The chief of Scottish Enterprise earns about £200,000 - double that of Finance Secretary John Swinney. The chief of every health body earns as much or more than Health Secretary Alex Neil who, like Mr Swinney, is on about £100,000. The highest earning chief executive is at Scottish Water, where the salary range reaches £240,000.
Alison Payne, research director for Reform Scotland, 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."
Spending on quangos is almost £12 billion, about one-third of the Scottish budget.
The think-tank says the money is largely beyond public scrutiny and calls for most quanogos to be re-integrated into government departments, giving ministers accountability for decisions.