Most of the victims of the killings, blamed on a vigilante group called the Davao Death Squad, were suspected drug pushers and other criminals.
The extra-judicial killings, however, were largely unsolved due to the absence of witnesses.
Deputy Ombudsman for Mindanao Antonio Valenzuela ordered the Southern Mindanao police command to immediately suspend Senior Superintendent Conrado Laza, former Davao City police chief, and Chief Inspectors Matthew Baccay and Vicente Danao and Inspector Filmor Escobal, heads of the San Pedro, Talomo and Sta. Ana police precincts.
Mayor Rodrigo Duterte, however, said he takes full responsibility for what is happening in the city, including the spate of extra-judicial killings.
"If they want to know something about those killings, they should ask me. I take full responsibility for the situation in my city," he said.
"Besides, there is something wrong with that order of the Ombudsman. How could you fault those officers when they were not even in their respective posts since the date they said the investigation was conducted? These officers were not even in their stations yet," he added.
Laza, who was appointed city police chief in June 2000, was replaced the other month.
Duterte said he will extend legal assistance to the four police officers.
The Ombudsmans order was based on the findings of a special task force which investigated the summary killings here.
At least 247 people were found to have been summarily killed from Aug. 1, 1998 to June 30 last year.
Of the cases, 67 fell under the jurisdiction of the Sta. Ana police precinct, and 52 and 51 under the San Pedro and Talomo police stations, respectively.
The Ombudsman faulted the four police officers for failing to respond to the killings.