Rural Affairs Secretary Fergus Ewing wrote to Colin Kennedy on the row over the interpretation of crofting law.
In the letter, seen by BBC Scotland, Mr Ewing warned action may be required if Mr Kennedy continued to adopt an opposing interpretation of the rules.
Mr Kennedy stands by the decisions made by the commission in the dispute.
He told BBC Scotland decisions taken were made after reasoned debate and consensus.
Common grazings are areas of land shared by crofters and others who hold a right to raise livestock on that land.
There are more than 1,000 common grazings covering tens of thousands of acres of land across Scotland according to the Crofting Commission, the public body overseeing the application of crofting legislation.
Grazing committees manage these areas of land and their members are elected by crofters.
Two grazings committees, one in Mangersta and another in Upper Coll, were dismissed by the commission earlier this year.
The commission, crofting's regulatory body, said finances related to the lands shared by crofters were not being managed according to the rules.
Crofters in Mangersta were later told by the commission that they could appoint a new committee.
A Scottish government spokeswoman said: "The Scottish government is committed to working constructively with the commission to ensure it delivers an effective service for crofting.
"The rural economy secretary recently wrote to the Crofting Commission to clarify the Scottish government's position in relation to Common Agricultural Policy funding and disbursal of funds by common grazings committees, and to stress the importance of the Scottish government and Crofting Commission moving forward together on these matters."
The Scottish government has disagreed with the Crofting Commission convener's handling of a dispute about the running of common grazing land on Lewis.