The killings, carried out in Manila from Wednesday to Thursday morning, came after police shot dead 32 drug suspects in the province neighbouring the capital early in the week in what was billed as a "shock and awe" operation against drug traffickers.
Manila police spokesman Senior Superintendent Erwin Margarejo said the 25 were killed in 18 various operations against drug suspects.
"It is a simultaneous police operation. All the units and stations of MPD (Manila police district) conducted their own operations," Margarejo told AFP.
Duterte on Wednesday praised the killings of the 32 suspects in Bulacan province, describing the operations as "good".
"If we could kill another 32 everyday, then maybe we can reduce what ails this country," Duterte said.
'Self-defence'
However national police spokesman Senior Superintendent Dionardo Carlos insisted that officers in Bulacan and Manila had killed only in self-defence.
"Can you blame the police now when the initial action is perpetrated by the suspect?" he said.
Duterte easily won last year's presidential election largely on a vow to kill tens of thousands of drug traffickers and addicts, which he said was necessary to stop the country's slide to narco-state status.
Police have killed more than 3,500 people in drug raids since Duterte came to office in the middle of last year, according to government data.
Unexplained circumstances
More than 2,000 other people have been killed in drug-related crimes and thousands more murdered in unexplained circumstances, according to the police.
He has also repeatedly assured policemen that he will protect them if they are charged for killing drug suspects as part of his campaign.
Rights groups have warned Duterte, who has said he would be "happy to slaughter" three million drug addicts, may be orchestrating a crime against humanity.
Wilnor Papa, Philippine human rights officer of Amnesty International, said the apparent uptick in killings this week appeared to be because of Duterte's calls for more deaths.
"Because of the remarks of the president, these kind of killings will go on," Papa told AFP.
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Philippine police kill 32 in 'shock and awe' drug raids
