MANILA - Philippine police murdered a town mayor while he was helpless in a jail cell, justice department investigators said Tuesday, contradicting claims by the accused and President Rodrigo Duterte that he was killed in a gunbattle. The accusations by the National Bureau of Investigation deepened concerns that police were carrying out summary executions as part of Duterte's controversial war on crime, which has claimed more than 5,100 lives in just over five months.

The NBI, equivalent to the US Federal Bureau of Investigation, said police shot dead mayor Rolando Espinosa and cellmate Raul Yap last month as they were defenceless in a provincial jail cell.

"After conducting an exhaustive investigation of the incidents surrounding the killing of Mayor Espinosa and Yap, the NBI concluded that the testimonies of several witnesses had disputed the claim of an alleged shootout between the (police) operatives and inmates Mayor Espinosa and Raul Yap but (was) a 'rub out'," the NBI said in a statement.

"Rub out" is a local expression, referring to the police killing a suspect and then saying he died in a gunbattle.

"The pieces of evidence, both testimonial and the forensic evidence all agree. We believe we have a very strong case," NBI deputy director Ferdinand Lavin told reporters.

Lavin said the NBI had recommended murder and perjury charges against 24 officers for their alleged role in the killings and subsequent lies.

The justice department will then decide whether to file the murder charges.

The accused police had claimed they fired in self-defence at the pair when they went into the jail cell before dawn to carry out a search warrant.

The police alleged Espinosa, who was in jail after being arrested in October on drug and gun possession charges, had a firearm and methamphetamine in the cell.

Lawmakers, media groups and human rights advocates had ridiculed that version of events, asking why police had to carry out a search in a jail cell at night and why CCTV footage of the event had disappeared.

They also asked how a man in jail could have a gun and drugs, and why he would shoot at police knowing he was outnumbered.

However Duterte, who has pledged never to let a policeman go to jail for waging his war on crime, repeatedly defended the officers involved.

Duterte had accused Espinosa, mayor of the town of Albuera in the eastern province of Leyte, of being a drug lord.

He had initially given police "shoot-to-kill" orders if Espinosa did not surrender, prompting the mayor to turn himself in.

In a speech late Monday, Duterte defended the police who killed Espinosa and said he believed their version of events.

"Do not force me to believe the theories and assumptions, even with the witnesses, that the mayor was killed (illegally) in the prison," he said.

Duterte had previously signalled he was happy Espinosa had been shot dead.

"You have here a guy, a government employee, using his office and money of government, cooking (illegal drugs) and destroying the lives of so many millions of Filipinos. So what is there for me to say about it?" he said last month.

Duterte's police chief initially stood down the police officer in charge of the raid pending an investigation, but the president immediately reinstated him.

Duterte, 71, won May elections in a landslide on a promise to kill tens of thousands of criminals to prevent the Philippines from becoming a narco-state.

His subsequent war on crime, in which an average of more than 30 people a day are being killed, has led to fears police are carrying out mass extrajudicial killings.

Duterte has repeatedly pledged to protect police from murder charges relating to his crime war, and pardon them if they are found guilty.