Tavish Scott said Prof Lorne Crerar told MSPs on Tuesday night that he is not allowed to speak out on the review, which includes of the work of HIE.
Mr Scott asked Economy Secretary Keith Brown if this was the case at a meeting of the Education and Skills Committee.
Mr Brown said he could not comment on private conversations.
In October, the Scottish government set out plans to reform Scotland's enterprise and skills agencies in a report on Phase 1 of its Enterprise and Skills Review.
It has proposed setting up a new single Scotland-wide statutory board to co-ordinate the activities of Scottish Enterprise and HIE.
The government said services already provided in the Highlands and Islands would be protected.
Last month, in an online statement, Prof Crerar insisted HIE will continue to exist in its present form despite changes to how it is overseen.
HIE provides support to businesses and initiatives in the Highlands and Islands, Northern Isles, Moray and Argyll.
On Wednesday, Mr Brown gave evidence to Holyrood's Education and Skills Committee on plans for Scotland's enterprise and skills agencies.
Mr Scott asked if Prof Crerar is allowed to speak out on the review, and also for a list of the organisations and the individuals who have backed a single statutory board.
The minister said all the submissions have been published and he said he would examine the minutes of the ministerial review group.
The chairman of Highlands and Islands Enterprise cannot speak out on the review of Scotland's enterprise agencies, a Lib Dem MSP has said.