"I believe that there is a chance that we will come to an agreement," Bayern's CEO, Karl-Heinz Rummenigge, told German magazine Kicker.
"We will have to play a waiting game and this is not something which will be resolved in the next two or three days."
The 22-year-old has a contract at Eastlands until 2015, having signed a five-year deal from German side Hamburg last summer, but the right-back has become frustrated at City and wants to play in the centre of defence.
After Munich signed Germany goalkeeper Manuel Neuer on a five-year deal on Wednesday, Boateng would solve Bayern's problems at centre-back and he has already told City manager Roberto Mancini he wants a more central role.
City are reported to have slapped a 20-million-euro ($28.8m) price tag on his head but Bayern's director of sport, Christian Nerlinger, has said they are only prepared to pay less than the 12 million euros Boateng cost City from Hamburg.
"I would like to go to Munich. On my side everything is clear," said Boateng.
Boateng wants to return to the Bundesliga to improve his chances of adding to his 13 caps, having last played for Germany in February's 1-1 friendly draw with Italy.
"I have already told Roberto Mancini that I want to play in central defence and not at right-back," he said.
"Bayern have indicated I will play in the centre. To play there regularly is important for me because I will have a better chance of playing in the national team. It is all about whether I am released. I hope it works.
"Bayern are bigger than City, they are one of the top six teams in Europe. To play for them would be an honour."
Boateng is suffering with a knee injury and his last appearance for City was in the FA Cup at Aston Villa in March.