Minister body recovered from the sea
His body was retrieved from wreckage of the light aircraft about 55m (180ft) underwater, Transport Secretary Mar Roxas told reporters.
He was described as a “most honourable” leader by the spokesman of President Benigno Aquino.
Three others were also on the plane when it crashed on Saturday.
Flags at government institutions and police stations are being flown at half-mast.
“The nation is united in grief and gratitude to one of her finest and most honourable servant-leaders,” Mr Aquino’s spokesman said in a statement.
The small plane was travelling from Cebu City in central Philippines to Mr Robredo’s hometown of Naga City, in Camarines Sur province, when it encountered engine problems.
The plane crashed just short of land in Masbate
The pilots sought permission for an emergency landing at Masbate province, but did not manage to make it there. Witnesses saw the aircraft crash into the sea less than a kilometre from the runway.
The bodies of the two pilots have also been found in the wreckage, the government said, but it is not clear if they have been retrieved.
A fourth person, Mr Robredo’s aide, managed to get out of the aircraft on Saturday. He was rescued by local fishermen and taken to hospital with minor injuries.
Mr Aquino flew to Masbate on Sunday to oversee the search and rescue operation for Mr Robredo, local media report.
The president was also with Mr Robredo’s family on Tuesday as they received his remains in Naga City.
Mr Robredo, 54, was in charge of the national police force and provincial governments. He was a close ally of Mr Aquino and helped his election campaign in 2010.
He was a long-time mayor of Naga City before his appointment to Mr Aquino’s cabinet.
A graduate of Harvard University’s John F Kennedy School of Government, Mr Robredo received numerous awards for good governance.
One of these was the prestigious Ramon Magsaysay award, known as Asia’s version of the Nobel prize, in 2000.
Various officials have described him as an “exceptional” and “inspirational” public servant.
“His unflagging sense of integrity and diligence served as an example to many of his colleagues in and outside government, and these same qualities have made him a most valuable and highly regarded member of President Aquino’s cabinet,” said Florencio Abad, budget secretary, in a statement. – BBC News