Van Gaal, who only months ago steered Bayern to a domestic league and Cup double and into the Champions League final in his first season in Munich, said Hoeness's comments over the weekend had been harsh.
"I do not want to contradict a man like Uli Hoeness as I have been at the club only a year and three months... but I feel a man with such importance for Bayern must be aware of the consequences of his statements," Van Gaal told reporters after arriving in Romania ahead of Wednesday's Champions League game against CFR Cluj.
"I am disappointed, very disappointed that my president says things like that about me. I always felt communication was one of my strong points," said the coach, who signed a contract extension to 2012 in late September.
"I am also surprised he would say these things now, at a difficult time when we have nine players injured."
Bayern issued a brief statement, soon after Van Gaal's comments, saying the two men had a frank discussion that included club CEO Karl-Heinz Rummenigge and other Bayern officials to clear the air.
"At the end of the discussion Uli Hoeness and Louis van Gaal shook hands and agreed to work responsibly together in the future for the good of the club," Bayern said.
Hoeness, who took over the presidency last year after three decades as Bayern manager, had criticised Van Gaal for overlooking several players including defender Martin Demichelis and Ukrainian Anatoliy Tymoshchuk for much of the season.
Both scored in their 4-2 league win against Freiburg on Friday in one of their rare starts for Bayern this season and have said they will leave if they do not play regularly.
Hoeness, who is no longer involved in day-to-day operations at the club, said Van Gaal should have used them earlier in the season to boost their confidence instead of pulling them off the bench when he ran out of players due to injuries.
Bayern have been plagued by injuries that have ruled out key players including wingers Franck Ribery, Arjen Robben, striker Miroslav Klose and captain Mark van Bommel among others.
They are top of Champions League Group E on nine points from three wins and a point on Wednesday would be enough to send them through to the round of 16 with two games to spare.
In the league, though, they lie seventh with 15 points from 10 games, 10 points behind leaders Borussia Dortmund.
Van Gaal signed a contract extension in late September to 2012.
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