Dortmund revealed the news on their Facebook page, although they were keen to stress they had yet to hear anything official from Bayern.
"Mario Gotze's agent Volker Struth told us a few days ago that the player wishes to make use of his release clause and on July 1, 2013 move to Bayern Munich," read the Dortmund statement.
Borussia chief executive Hans-Joachim Watzke admitted he would be sorry to see Gotze go but admitted the player had not broken his contract to secure the move.
"We are obviously disappointed beyond measure, but emphasize that both Mario and his advisers have behaved within the terms of the contract," he said.
"From Bayern Munich there has been nothing official on this matter up to this date."