The newly-crowned Bundesliga champion announced on Tuesday that the club has agreed personal terms with the Germany international and will match his 37 million euro buyout clause to complete the deal.
Watzke is not impressed with the way Bayern has dealt with the situation, though, and has accused the club of deliberately trying to weaken its rivals.
"I believe Bayern have followed the same pattern to achieve success for quite a while and weakening their rivals is part of their strategy," Watzke told Sport Bild. "We always expect approaches from Munich for our players, regardless of their statements of solidarity.
"We try to fight them with the means we have. It's then up to the players to decide which is the more interesting prospect for them."
Gotze, 20, is a product of the Dortmund youth academy and has made over 100 official appearances for BVB so far.
The attacking midfielder's contract with the Schwarzgelben was due to expire in the summer of 2016.