Gotze is in Joachim Low's squad for the upcoming World Cup qualifiers against Republic of Ireland and Sweden, despite having only recently returned from an ankle injury.
He has come off the bench late on in Bayern's last two matches.
Hoeness was quoted in the Bild newspaper as telling Kicker: "For everyone involved it would be better if he were to train fully for two weeks, then he would be physically where he needed to be."
But the Bayern chief added: "That is my personal opinion. I don't interfere."
Low on Monday called Heiko Westermann into his squad as a replacement for the injured Sven Bender, the German Football Association announced.
Bender has withdrawn from the squad after picking up a muscle strain in Borussia Dortmund's defeat to Borussia Monchengladbach at the weekend.
Germany take on Ireland in Cologne on Friday before travelling to Stockholm to take no Sweden the following Tuesday.