No casualties were reported in the explosions, which witnesses said tore through the logistics building of the National Capital Region Police Command in the Camp Bagong Diwa police complex in eastern Manila shortly before midnight on Monday.
The building was still on fire nearly an hour later, with the menace of exploding munitions preventing firemen from approaching the area.
"The ammunition dump exploded, causing damage to several nearby buildings," national police chief Arturo Lomibao said.
The dump contained explosives, bullets and firearms, he added.
"There is no indication" of sabotage, he said. "Based on evidence this was not caused by an enemy attack."
He said police did not know the cause of the blasts. "We should find out in due time," he added.
Police in Manila had been placed
on high alert
The blasts occurred shortly after President Gloria Arroyo flew to New York to attend a general assembly meeting of the United Nations.
Lomibao said it was just a "coincidence" that the fire occurred shortly after she left.
Police in Manila had been placed on high alert amid rumours of possible destabilisation attempts following the defeat of an impeachment complaint against Arroyo last week for alleged election fraud.