The first blast happened along Norzagaray Street corner Elizondo Street in Santa Cruz, Manila, near the Manila Golden Mosque at 5:55 pm on Saturday, killing two people and hurting 4 others, police said.
Explosives Ordinance Disposal teams have reportedly been deployed to the blast area to secure the Islamic Center in Quiapo.
Coronel said Macaraya helped plant the bomb to avenge his teenage nephew that was mauled by several individuals from a group with the last name "Kahulugan".
The first blast damaged part of the Islamic centre and shattered windows in nearby buildings, according to the AFP photographer and witnesses.
Initially, authorities feared that either communist insurgents or militants linked to Islamic State may have been responsible for the latest bombings.
The Philippines is a mainly Catholic country but it has a significant Muslim minority, some of whom live in Quiapo.
WEATHER: Fine, becoming partly cloudy
An inch or two of snow could fall above the 5,000-foot level, and there could be trace amounts as low as 4,000 feet. A late spring storm moved into the region early Saturday , bringing cloudy skies and scattered showers.
It was learned that a delivery man was carrying the said "package" and it was turned over to Abinal's aide even before it exploded, which caused their instantaneous death.
The police tightened security in the area following the blasts that investigators claimed were not the handiwork of terrorists. The two dead were identified as the person who delivered the package and the one who received it, he said. "Our prayers go out to those who perished, and we extend our sympathies and deepest condolences to their loved ones", it said in a statement.
On April 28, another explosion injured 14 people in Quiapo as South-east Asian leaders were meeting for a summit a few kilometres away. Police said it was a pipe bomb explosion and was not a terror attack.
It also expressed grief over the loss of lives in the explosions. Police earlier said the first explosion originated from a package delivered to the lawyer's office. "But nevertheless, whether they are ISIS or not, they are still the same bandit group who are out to terrorize the country", he said.
The IS group claimed its fighters killed "five Shiites" in a bombing in Manila.