A report by the Public Audit Committee called for "clarity" from the Scottish Government on how new arms-length foundations will operate.
Under current plans, colleges are transferring money that was previously held as surpluses into charitable foundations.
The move follows the UK-wide reclassification of further education colleges as public bodies.
Because the new foundations will be independent of colleges, the committee expressed reservations there would no longer be proper scrutiny and accountability over public funds. Hugh Henry, convener of the committee, said: "In Scotland, colleges will be able to create foundations so they can transfer any current accumulated cash reserves and any future annual surpluses... for use in future years.
"These foundations will be required by statute and by the Scottish Charity Regulator to operate in their own best interests, but our committee is concerned that this independence may be to the detriment of individual colleges. The Public Audit Committee is calling on the Scottish Government for clarification on how it will manage the risk that the priorities of foundations could diverge from the priorities of relevant colleges."