Sammer lost his temper after Bayern's 2-0 win over Werder Bremen last weekend, criticising the team's performance for 80 minutes of a game which was won in the last 10 minutes.
The tone he used was not to Heynckes' liking and he insinuated that Sammer had gone too far with his criticism.
Internal friction has been mentioned as a possible cause for their midweek Champions League loss, but Hoeness says he will not condemn Sammer's actions.
"If everybody goes to sleep, we won't win anything," he said. "Good performances only come from friction.
"This is always going to be a problem when you have a strong-minded director of sport, which we now have, fortunately - there are always going to be differences of opinion.
"When you are a bit sensitive, like Jupp is sometimes, then of course it can cause a stir, but I would not get worked up about it."
Hoeness appears to take Sammer's side in the argument, which both parties have declared will not have any repercussions.
He told Munich's Tz and Az newspapers that it "is Sammer's job to put the gloves on now and again".
He added: "That is what I did for 30 years. He is on the same level as Heynckes."
Hoffenheim may just be the right opponents for Bayern to level their record for consecutive wins at the start of the season tomorrow [Saturday], having beaten Markus Babbel's side 7-1 last season.
Babbel does not have the best of records in Munich as a coach, losing 4-0 with his former club Hertha Berlin last season.
Furthermore, Hoffenheim have never managed to beat Bayern in eight attempts.
However, their primary concern remains the health of midfielder Boris Vukcevic, who was involved in a car accident last week and is still in a coma.
"It is not easy to prepare for a Bundesliga game in these conditions, but we have got to try to prepare as usual," said Babbel.