The mayor was one of some 160 officials Duterte put on a so-called "narco-list" as a war on drugs that has claimed more than 3,000 lives accelerates. Another mayor was killed in an alleged shootout with police.
Filipino police shot dead a mayor and another man in jail in an apparent gun battle as they were searching for weapons and drugs,. It was the second narcotics-linked death of a local politician in a week.
Rolando Espinosa, mayor of Albuera town in Leyte, turned himself into authorities in August after President Rodrigo Duterte publically named him and his son Kerwin drug traffickers and gave "shoot on sight" orders to police if the two resisted arrest. The mayor was later released, only to be indicted and imprisoned last month.
Espinosa was one of some 160 officials Duterte put on a so-called "narco-list" as he accelerates a war on drugs that has claimed more than 3,000 lives.
Police said they recovered two pistols, methamphetamine and drug paraphernalia from the prison raid. It remains unclear how the mayor and other man acquired the weapons and drugs in prison.
The president's office called Espinosa's death "unfortunate" and pledged to investigate.
Espinosa denied any links to drugs, but his son Kerwin is an alleged drug kingpin in the Eastern Visayas region. He was arrested by Abu Dhabi police last month and is expected to be extradited.
Last week, Samsudin Dimaukom, the mayor of another town, was killed in an alleged firefight with police that also left nine of his men dead in the southern Philippines. Duterte also named him on the "narco list."
During more than a quarter of a century as mayor of Davao, the country's second-largest city, Duterte built a reputation for being hard on crime, a policy that earned him criticism for rights abuses but also praise for turning Davao into a safe city with better services.
Duterte took over the presidency in June promising to go after the drug trade, which he says is a pandemic that has corrupted politics, the military and ruined lives.
The extent of the crackdown involving both police and vigilantes has led to warnings from the West and human rights organizations over the rule of law and extrajudicial killings.
Undeterred, Duterte has vowed to press on with the drug war and verbally assaulted his critics, including US President Barack Obama.
While a controversial figure abroad over the drug war and caustic rhetoric, Duterte remains popular at home. According to a poll last month, after three months in office his approval rating stood at 86 percent.