Duterte, who has promised to rid the country of illegal drugs and criminality within six months, said in a speech that he has ordered an investigation, and accused the generals of committing a crime that is tantamount to treason.
Two of the men are retired and the three others are in active service.
"I order them relieved from their assignment and to report to the director general," Duterte said, adding that he expects action from the police commission that investigates erring police officers.
Officials said since Duterte took office on June 30, at least 30 suspected drug pushers have died in clashes with police, bringing the number of drug suspects killed in such gunfights since the May 9 election to more than 100.
The five generals he named included Chief Supt Vicente Loot, who retired as director of the police training service and is now a town mayor.
Loot, in an interview with the ABS-CBN network, said the accusations against him were bogus and he had been cleared of wrongdoing earlier by the national police's anti-illegal drugs task force.
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