Regional police chief Elmer Beltejar said police were patrolling near the house of Mayor Rolando Espinosa Sr in the central town of Albuera when they were fired upon by the mayor's bodyguards. The police fired back, killing six bodyguards, he said.
The clash came a day after Espinosa surrendered to national police chief Ronald dela Rosa. Authorities allege he has been protecting drug dealers, including his son Erwin, whom he urged to surrender.
National police spokesman Dionardo Carlos said authorities are looking into reports the younger Espinosa has fled the country.
As the number of suspected drug dealers and users killed in his crackdown rose to more than 400, Duterte said he will not stop his anti-drug battle even at the risk of losing his presidency.
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He said he has asked for rehabilitation centers to be opened in regions across the country to accommodate the thousands of surrendering drug users.
Duterte took office June 30, and since then 402 suspected drug traffickers have been killed in clashes with police, national police records show. At least 4,418 others have been arrested.
Duterte, a former prosecutor and mayor of southern Davao city, where he built a reputation for tough anti-crime methods, won the presidential election earlier this year on a promise to end criminality and corruption in the first three to six months of his presidency.
The moves have sparked alarm among human rights and anti-drug groups.
Yury Fedotov, the executive director of the U.N. Office on Drugs and Crime, condemned the government's apparent endorsement of extrajudicial killing, which he described as illegal and a violation of fundamental rights.
"Such responses contravene the provisions of the international drug control conventions, do not serve the cause of justice, and will not help to ensure that 'all people can live in health, dignity and peace, with security and prosperity,'" he said in a statement.