Around 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.
Think-tank Reform Scotland carried out the study and believes quangos "are not sufficiently accountable to the Scottish Parliament or the Scottish people".
The 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.
It found 43 executives are paid more than the First Minister, 132 are paid more than a Cabinet Secretary and 686 more than an MSP.
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.
A Scottish Government spokesman said the number of quangos has been reduced in recent years.
He said: "Pay ranges are assigned in relation to the roles and to support the recruitment and retention of staff."