Paulo Fonseca thinks referee Federico La Penna showed AC Milan "a lack of respect" during their 2-1 defeat by Atalanta.
Ademola Lookman's late strike settled the contest at Gewiss Stadium, where Alvaro Morata cancelled out Charles De Ketelaere's earlier effort.
While Atalanta climbed to the Serie A summit following a ninth straight win, Milan saw their seven-game unbeaten streak across all competitions come to an end.
However, Fonseca suggested his side were on the wrong end of questionable officiating, including for the hosts' first goal, where he felt De Ketelaere pushed Theo Hernandez while climbing to head home.
"I am not afraid to speak the truth," he told Sky Sport Italia. "I have always respected the work of the referees. I realise they have a difficult job, but every week, it is always the same.
"The way the referee officiated throughout this evening was a lack of respect for Milan.
"The first goal, [there] was a clear foul, there is absolutely no doubt. The way the referee officiated throughout was against Milan, there is no doubt."
Although, Fonseca acknowledged poor defending from set-pieces proved costly for his side.
"At the end of the day, we lost the game on two set-plays," he added. "The first half was very good, but in the second, we didn't have that link with the strikers.
"I think we deserved more tonight, it was tough to accept conceding two goals from dead-ball situations."
Meanwhile, Atalanta coach Gian Piero Gasperini revelled in his side's victory, which lifted them to the top of the table and already had their supporters chanting songs about winning the Scudetto.
"Naturally, this is a great victory against a team with undoubtedly very talented players among the best in the league, and we thoroughly deserved the win," he said.
"The people of Bergamo have their feet firmly on the ground, so don't take anything for granted. If we were still up there after another 20 games, it'd be different, but as things stand, it is an expression of joy and a deserved one, too."