Boateng was strongly linked with a move to Manchester United before the English transfer window closed, while a number of other clubs are believed to be monitoring proceedings.
The Germany international played the full 90 minutes of Bayern's 1-0 win over Drochtersen/Assel in the DFB-Pokal on Saturday afternoon, but Kovac suggested after the match that an exit could still occur.
"If anything happens at the end of the transfer period then we see, it may happen," Kovac told reporters. "But I'm going to assume that nothing happens, I'm glad that he got through this game very well."
Boateng has made over 250 appearances for Bayern since a 2011 move from Manchester City.