Flamini has been strongly linked with a loan move to the Barclays Premier League club in the January transfer window.
"We have heard rumours regarding possible interest from Manchester City for Flamini," AC Milan sporting director Ariedo Braida said.
"But for the time being, there has been no official offer, interest or talks between AC Milan and Manchester City.
"Flamini is an AC Milan player."
The former Arsenal star has struggled to earn a regular place with the Rossoneri this season, making just eight Serie A starts for Leonardo's side, and he is desperate to play first-team football in a bid to keep his hopes of a World Cup place alive.
The 25-year-old joined Milan in May 2008 from Arsenal and is under contract with the Serie A giants until June 2012.