Reynaldo Parojinog, mayor of the city of Ozamiz on Mindanao island, was killed with his wife and 10 others at his home as police served a warrant.
According to a ranking Ozamiz City official, the Parojinogs had a feeling the police were out to kill them.
Speaking to Agence France-Presse, Superintendent Lemuel Gonda said: "Police were serving a search warrant when the security guards of the mayor fired at them, so our policemen retaliated". They said they recovered a cachet of rifles, cash and illegal drugs inside.
"The Parojinogs, if you would recall, are included in President Duterte's list of personalities involved in the illegal drug trade".
His wife, Susan, and five other people were also killed, and a second raid at another house owned by the family left five more people dead, police said.
More than 7,000 people are said to have been killed since Mr Duterte launched a war on the drugs trade in July 2016.
Authorities said Parojinog and others were killed in an exchange of gunfire with police.
All three mayors were among more than 160 officials Duterte named publicly as being linked to illegal drugs in August past year as part of a shame campaign.
Following the raid police arrested Parojinog's daughter, the city's vice-mayor, and said she would face charges.
Venezuela: Protesters, troops clash ahead of Sunday vote
Several countries and global organizations, including the USA and European Union , have condemned the vote for Sunday. Maduro is aligned with the political movement of Hugo Chavez , the President from 1999 until his death in 2013.
Senate Minority Leader Franklin Drilon questioned the circumstances surrounding the deaths of Parojinog and Rolando Espinosa, Mayor of Albuera, who was killed last November.
Two councilors of Ozamiz City on Monday will temporarily assume the posts of mayor and vice mayor following the death and arrest of their city's officials.
Also yesterday, Justice Secretary Vitaliano Aguirre II ordered the immigration bureau to be on the lookout for seven suspected illegal drug operators, including at least two publicly linked by Duterte to the narcotics trade.
In both the Espinosa case and the Parojinog raids, police and CIDG agents served the search warrants before dawn.
Ozamiz City Police Chief Senior Inspector Jovani Espenido said at the media briefing that Parojinogs were the source of illegal drugs in Ozamiz. The police have claimed that they killed suspects only in self defence.
Presidential Spokesperson Ernesto C. Abella, in a statement yesterday, reiterated this, saying: "The Administration vowed to intensify the drug campaign".
Relatives even said that Parojinog did not spare those he suspected to be involved in illegal drugs, including his kin.
Duterte, in several of his news conferences and public events, has waved a thick book he said contained names of officials suspected of drug links.