Kovac, 48, was dismissed by Bayern on November 3 in the wake of a 5-1 thrashing at Eintracht Frankfurt, AFP reported.
Interim coach Hansi Flick oversaw a 2-0 home win over Olympiakos in midweek, with Bayern qualifying for the last 16 of the Champions League with two games left, and Saturday's 4-0 league thrashing of Dortmund at the Allianz Arena.
Kovac won the Bundesliga and cup double last season, but was sacked after 16 months and Hoeness confirmed to broadcasters ZDF late Saturday the Croatian coach had lost the backing of his dressing room.
"There were certainly elements within the team that wanted the coach gone," revealed Hoeness without naming who, although forward Thomas Mueller had said he was unhappy to be repeatedly benched by Kovac.
"That's why the club leaders reacted accordingly."
Hoeness said Kovac himself admitted it was "the right decision" to part company.
In an interview with Sky earlier, Hoeness said he remains in contact with Kovac, "as far as I am concerned, the coaches almost always leave as friends. He's not happy, of course, but I think he's also relieved."
Hoeness, who will step down after a decade as Bayern president on Friday at the club's annual general meeting, said "absolutely no decision has been made" as to who will replace Kovac.
Both Hoeness and club chairman Karl-Heinz Rummenigge hinted after Saturday's game Flick would stay on past the November 23 deadline – Bayern's next league game – which Hoeness had set as a date to announce a new head coach.
Both Ajax coach Erik ten Hag, who coached Bayern's reserves from 2013-15, and Paris Saint Germain's German coach Thomas Tuchel have said they will not leave their respective clubs this season.
Former Arsenal manager Arsene Wenger has also criticized Bayern's lack of discretion for putting out a statement saying it turned him down.
The 70-year-old Frenchman insisted he spoke to Rummenigge by phone and only expressed interest in the job in a brief conversation when the pair agreed to speak again next week.
"I think we both misunderstood and I am sorry for that," Rummenigge told reporters, adding he will phone Wenger in the coming days to "clear this thing up."
With two wins under Flick, Bayern has time during the upcoming international window, "which we need to get a clear idea what we want", said Hoeness, adding the goal must be a "long-term solution."
"Until such a solution comes, I am of the opinion that Hansi Flick is not a bad solution."