Helicopters and divers were searching Sunday for one of the most powerful Philippine politicians, feared dead after a light aircraft he was travelling in crashed into the sea.

President Benigno Aquino took the lead in the search for Interior Secretary Jesse Robredo, a day after his plane went down about a kilometre (0.6 mile) from the central island of Masbate.

Aquino flew to Masbate where military divers and helicopters were scouring the area for the minister, a close presidential aide, who is missing along with two pilots.

Transport Secretary Mar Roxas, who accompanied Aquino, said special sonar equipment had been flown to Masbate to help in the search operation after some debris, including one wing of the missing plane, was recovered.

"We remain hopeful that Secretary Robredo was just carried by the current... and that he will be found," Roxas said, adding that Aquino is "very emotionally attached to Jesse and he is doing everything he can".

The twin-engine Piper Seneca, carrying Robredo, his aide, and two pilots—one of them a Nepalese student pilot—went down after developing engine trouble.

Robredo's aide, Jun Abrazado, was the only rescued survivor and Aquino said he was conscious and had sustained only a few injuries.

Abrazado said when the plane hit the water, he unfastened Robredo's seatbelt and tried to help him out but water quickly filled the aircraft, ABS-CBN television reported.

Masbate Vice Mayor Allan Cos later told the channel that an object, which might be the wreckage, had been spotted some 200 metres (660 feet) underwater but it was too deep for divers to reach.

The government called a prayer vigil at a Roman Catholic chapel in Manila for the 54-year-old cabinet member, a father of three daughters and a former city mayor.

As interior secretary, Robredo was in control of the country's 143,000-strong national police force which has long been dogged by accusations of corruption and abuse.

In recent months, he had ordered investigations into alleged financial irregularities over the construction of police stations and purchase of helicopters and rescue boats.

Robredo was also playing a key role in the dismantling of private armies allegedly deployed by some powerful provincial governors and city mayors ahead of congressional and local elections in 2013.

A former official at an ice cream company, Robredo was elected mayor of Naga City in the strife-torn Bicol region, south of Manila in 1988 at the age of 29, making him the youngest mayor in the country at the time.

His success in turning the once-sleepy city into a trading, housing and education centre won him many honours including a 2000 Ramon Magsaysay award, considered Asia's version of the Nobel Prize.

After serving nine years as a city mayor, he joined Aquino's successful campaign for the presidency in 2010, endorsing his reformist platform. Robredo was subsequently appointed to the cabinet.