Thomas Tuchel was reportedly in the running for the vacancy only for Bayern CEO Karl-Heinz Rummenigge to confirm the former Borussia Dortmund coach - strongly linked with Paris Saint-Germain - has agreed to move elsewhere.
But despite Kovac seemingly being the next man in the Allianz Arena dugout, Bobic, who is the member of the club's management board overseeing sport, says he is unaware of a deal being done for the 46-year-old Croatian.
"I'm just coming back from Denmark," Bobic told Bild. "I haven't received a call.
"Niko always talks to me but I haven't received any information."
Bayern have indicated the club will make an announcement regarding Heynckes' successor by the end of April, with the 72-year-old on track to depart with another treble to his name after claiming the Bundesliga, DFB-Pokal and Champions League titles at the end of his previous spell in 2013.
Kovac - whose side are set to visit the Allianz Arena on April 28 - has led Eintracht to their current fifth placed standing in the Bundesliga table. They sit two points outside the Champions League places, to last season's DFB-Pokal final, which Dortmund won 2-1.