An initial blast occurred at about 6:00pm (1000 GMT) near a Muslim mosque in Quiapo, one of the older parts of Manila where there are big slums, a police report said.
That blast killed two and injured four, according to the report.
A second explosion occurred in the same area around 8:30pm, according to an AFP photographer who was among a group of journalists near the scene.
The second explosion did not cause major damage to any of the shops or other buildings in the street, according to the AFP photographer.
But it appeared to injure a policeman who was inspecting the body of one of the victims of the first blast, according to witnesses.
Another explosion in Quiapo on April 29, which occurred as Southeast Asian leaders were meeting for a summit, injured 14 people.
The Islamic State group claimed responsibility for the April 29 explosion, but police insisted it was not a terrorist attack, nor was it related in any way to the gathering of political leaders.
They said people involved in a private grievance used a pipe bomb in that blast.
Police did not immediately give any explanation for Saturday's explosions.
Militants who have pledged allegiance to the Islamic State group are based in the southern Philippines, more than 800 kilometres (500 miles) from Manila.
Those militants mainly operate in the south, although they have been blamed for terrorists attacks in Manila.
The Abu Sayyaf group, which is most infamous for kidnapping foreigners and killing them if ransoms are not paid, was blamed for the bombing of a ferry in Manila Bay in 2004 that killed more than 116 people.
(Except for the headline, this story has not been edited by NDTV staff and is published from a syndicated feed.)