Munich newspaper the Muenchner Merkur claims Germany international Boateng, currently injured, has agreed terms to join Bayern for next season. Munich's director of football Christian Nerlinger refused to confirm the report.
Boateng, who has 13 caps for Germany, could cover at right back and play at centre half for Bayern.
"It's not correct that we've already agreed terms. We're keeping tabs on him, but that's difficult now because of his injury," Nerlinger told the Merkur.
Boateng's advisor Joerg Neubauer also played down the reports.
The 22-year-old is under contract in Manchester until June 2015, but a knee injury has restricted his appearances this season and City are reported to be reluctant to let him go.
"We have big plans with Jerome," City's technical director Mike Rigg told German daily Bild.
"He's an important part of our plans for the future.
"We'll be playing Champions League qualifiers next term and want to do so with Jerome. He's not for sale."
Bayern are also reported to be monitoring City's Togo striker Adebayor, who is on loan at Real Madrid.
The 27-year-old is seen as a possible replacement for 32-year-old Germany striker Miroslav Klose, who is out of contract at the end of June.
"Real have a purchase option (on Adebayor)," said Rigg, with Adebayor reported to be worth 13 million euros ($19.3m).
"Adebayor is a guy who would fit in at Bayern. He's a great player, similar to (ex-Bayern striker) Luca Toni."
Reports have also linked the second division's top-scorer, Nils Petersen of Energie Cottbus—who has scored 24 goals in 31 games this season—and Borussia Moenchengladbach midfielder Marco Reus to Bayern.