About 130 people working for public bodies receive more than a Cabinet Secretary's salary of £101,000, while almost 700 are paid more than an MSP's salary of £58,000.
The think-tank Reform Scotland, which carried out the study, believes quangos "are not sufficiently accountable to the Scottish Parliament or the Scottish people".
Quasi-autonomous non-governmental organisations lead the delivery of public services in Scotland including culture, healthcare, the environment and justice.
They are managed by boards whose members are directly appointed by Government ministers.
Freedom of Information requests were sent to all 72 of Scotland's quangos, with 61 replying. Some 43 executives are paid more than the First Minister, 132 are paid more than a Cabinet Secretary and 686 are paid more than an MSP.
Although health boards are classed as quangos, only the salaries of board members were taken into consideration for the report.
Reform Scotland believes all quangos, with the exception of tribunals, should either become fully independent of government or have their functions transferred to existing government departments. Research director Alison Payne said: "Scotland needs to end its love affair with quangos."
The Scottish Government said since October 2007, the number of devolved public bodies had reduced from 199 to 113, exceeding the Government target of a 25 per cent reduction."