Gotze is in Joachim Low's squad for the upcoming World Cup qualifiers against Republic of Ireland and Sweden, despite having only recently returned form 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Bender has withdrawn from the squad after picking up a muscle strain in Borussia Dortmund's defeat to Borussia Monchengladbach at the weekend.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.
Bender's Dortmund team-mate Marco Reus was also forced to pull out of the squad on Monday with an ankle injury, leaving coach Low with a 20-man party for the clash with Ireland.
The squad met on Monday in Dusseldorf and will remain in the North-Rhein Westphalian capital until Friday night's game in Cologne, after which they will spend two more days in the city before travelling to Sweden for their final qualifying fixture.
Germany need a win from either of their final matches, or just a draw against Sweden, to qualify for next summer's World Cup.