An initial blast occurred at about 6:00 PM (local time) 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 8:30 PM, 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.
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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 today's explosions.
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.
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