The Dutchman said that the Allianz arena crowd often resembled a theatre audience, something they shared with supporters at his previous clubs Barcelona and Ajax Amsterdam.
"It's very bad," the often volatile Van Gaal told reporters on the eve of a potentially decisive Bundesliga match at home to VfL Bochum.
"It's like Barcelona and Ajax, a theatre public.
"Of course, in the last three weeks it has been a surprise but when we win everything, it's easy to have voices.
"I think the public must get behind the team when things go badly, and that is something I haven't experienced," added Van Gaal, who exempted the South Curve supporters from his criticism. "They are always getting behind the team," he said.
Bayern, who made a poor start to the season, could still win the Bundesliga, Cup and Champions League.
They are level on points with Schalke 04 at the top of the Bundesliga with two matches to play but have an easier run-in and a superior goal difference.
They face Werder Bremen in the German Cup final and Inter Milan in the Champions League final.
A win against Bochum coupled with defeat for Schalke at home to Werder Bremen would all but clinch the Bundesliga for Bayern.
