Dortmund boast the largest standing area in Europe, the Suedtribune (South stand), which produces an intimidating wall of noise, but Buerki was less impressed with the support from other parts of the stadium.
"The South stand is always there and always support us," the Swiss told reporters.
"But the people in the East and West stands come to the stadium to boo their own team. I don't hear any support from those two stands. They would be better off staying at home.
"We play the ball backwards and the whistling begins," he added. "These are people who have no knowledge about football. Perhaps they have nothing better to do."
Dortmund forward Pierre-Emerick Aubameyang, linked with a move to Arsenal in the January transfer window, made his first appearance of the year after being dropped for the last two games but he failed to add to his tally of 13 league goals.
"We have said we are ready to agree to a transfer if certain conditions are met," Dortmund sporting director told Sky Sport Germany.
"Either they meet our conditions and there can be a transfer or they won't be met and Aubameyang stays here until the summer.
"That's what his family have been told and they have accepted it."
(Writing by Brian Homewood in Berne, editing by Ed Osmond)
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