Sammer said the side had "lacked emotion" and were "hiding behind the coach" after a disappointing performance which was nevertheless rewarded with three points.
Hoeness on Monday told the Bild newspaper that there was no need to be so critical, suggesting that their Bundesliga rivals will now be laughing at them.
"If you do it so often, then it loses its effect," Hoeness said.
"At this moment in time, it was unnecessary."
Hoeness himself developed an uncompromising reputation during over two decades as the club's director of sport and Sammer, who vented his anger in a similar fashion at the same stage of last season, in spite of a record-breaking start to the campaign, appears to be keen on emulating his peer.
"All he's done is give the impression that we have got to apologise for a comfortable 2-0 win," added Hoeness.
"It gives an impression of Bayern Munich which really isn't good. It's as if we'd lost three and drawn two out of five games. In Dortmund, they'll be rolling around laughing."
Hoeness is to summon Sammer to his office this week to set the record straight, probably by showing him the latest league standings which have Bayern just points from the summit after four wins and a draw.
"There are some people who used to play football themselves who seem to have forgotten how it is after international matches," added Hoeness.
"You can't be in top form now, and we've had lots of injuries too."