The Germany international has struggled to make an impact at the Allianz Arena following his move from Borussia Dortmund in 2013 and has been linked with a move to Juventus this summer.
He was widely criticised for his form last season and recently suggested there wasn't enough communication between himself and coach Pep Guardiola.
Gotze later added that he had been mis-quoted, but his representative Volker Struth has now admitted his future is less than certain.
"Mario has hinted that his situation at Bayern in the last two seasons has not been ideal," he told Tuttosport. "But it is also true that until now no club has come forward with an economic proposal.
"Bayern has rejected talk of a possible transfer, though we don't want to say there is no chance of staying or going abroad.
"Still there is time before the close of the market, so anything can still happen."