The body of Philippines Interior Secretary Jesse Robredo has been recovered from the sea off a central province where his small propeller plane crashed three days ago.

Mar Roxas, the transport secretary, said that Robredo's body was pulled out of the water early on Tuesday morning from the fuselage of the twin-engine Piper Seneca, 55 metres underwater and about 800 metres off Masbate province.

The bodies of the Filipino pilot and a Nepalese student pilot flying with him were in the cockpit and would be retrieved later, Roxas said.

"Sad as it is, we are now in search and recovery and retrieval," he said.

Robredo, 54, was heading to his hometown of Naga City from central Cebu City on Saturday when one of the plane's engines stalled. The pilot attempted an emergency landing at the Masbate airport but crashed in the water.

An aide of Robredo travelling on the plane managed to escape as it sank and was rescued by fisherman and later helped in the search, Roxas said.

Robredo had been mayor of Naga City before being selected by reform-minded President Benigno Aquino as secretary of interior and local government. As interior secretary, Robredo was also in charge of the police.

During his career, Robredo developed a pragmatic and honest reputation and became a rare official to earn respect from the public, deviating from the political patronage and corruption that characterised traditional politicians.

He had even won Ramon Magsaysay award, regarded as Asia's version of a Nobel Prize, in 2000 for good governance.