|Philippine President Benigno Simeon "Noynoy"|
Aquino said raids on suspected safehouses of terrorists have yielded nothing so far.
He said there have always been unsubstantiated reports of terror threats, bu the difference in the last few days is there have been sightings of terrorists and explosive devices.
Aquino said the threat remains for so long as the suspected terrorists have not been arrested and no case has been filed in court.
Police earlier said they were hunting Islamic militants who may still be planning to attack the nation's capital, even after the Black Nazarene procession went ahead without incident.
President Aquino had warned that militants were planning to bomb Monday's spectacular annual festival, when an estimated 8 million pilgrims converged on Manila in a bid to touch the alleged centuries-old icon of Jesus Christ.
The feared attack in Asia's Catholic outpost did not take place after heavy security was imposed in the city, but national police chief Nicanor Bartolome said on Tuesday that there was still a threat.
"Metro Manila remains on full alert," Bartolome told reporters, adding between 6 and 9 suspects were being tracked.
"We are conducting surveillance on certain houses," he said without giving further details.
National police spokesman Agrimero Cruz also said safety measures put in place for the procession would remain on Manila's mass public transport services, as well as its airports and the city's port.
"We apologize to the public over the measures that are in place to protect the majority. These are being undertaken with public safety and security in mind," Cruz told reporters. "We can't say how long these will last."
The government had said the suspects may be members of the Al-Qaeda-linked Abu Sayyaf, blamed for the country's deadliest terrorist attacks, or the Moro Islamic Liberation Front (MILF).
The front has been waging a separatist rebellion in the south since the 1960s that has claimed tens of thousands of lives.
Its leaders are currently involved in peace talks with the government and have disavowed terrorism, but have previously acknowledged an inability to control "rogue" members.