Blasts ripped through shops and pavement stalls on Saturday night in the historic Quiapo district near the Golden Mosque, a well known landmark in the city.

Police said on Sunday the bombs were designed to target a "specific individual" but declined to provide details.

The first bomb exploded after a motorcycle rider delivered a package to an unidentified man. Both men were killed.

Two hours later, another bomb exploded in the area, injuring emergency services workers.

"There is no indication of a terrorist attack," a police commander told reporters.

Authorities urged the public to remain vigilant and report any suspicious activity.

"Your authorities are on top of the situation," said director Oscar Albayalde, head of Manila's police force.

"I have ordered all our policemen on the ground to stay alert and focused in securing their areas of responsibility."

Presidential spokesman Ernesto Abella called for calm following the blasts.

"We are saddened by the loss of lives brought by yesterday's night explosions in Quiapo," he said.

"While [the] investigation is now ongoing, we ask the public to remain alert and immediately report to authorities any suspicious activity or movement."

A pipe bomb exploded in the same area on April 28, injuring 15 people, as South-east Asian leaders gathered in Manila for a summit.

Initially, authorities feared that either communist insurgents or militants linked to Islamic State may have been responsible for the latest bombings.

with DPA