The 29-year-old prince, known in the military as Flight Lieutenant Wales, has previously co-piloted RAF Sea King helicopters and will now be able to command operations, Clarence House, the official residence for Prince William said in a statement.
"Flight Lieutenant Wales, as he is known in the military, will now command search and rescue operations in RAF Sea King helicopters," it said.
The Duke of Cambridge passed the tests on May 29.
The prince completed two days of ground and air-based tests to achieve the qualification, following his two years of flying experience in the helicopter.
The mock rescue scenarios saw him take part in an airborne search for a yacht, two missing kayakers, people out at sea and extinguishing a simulated fire on a large survey vessel, the Daily Mail reported.
He joined C Flight, 22 Squadron after graduating training in September 2010.
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Wing Commander Mark Dunlop, the squadron's commanding officer, said, "Flt Lt Wales demonstrated the required standards needed for the award of operation captaincy".
Earlier this year the prince spent six weeks flying search-and-rescue missions from the Falkland Islands. The deployment came amid growing tensions between Argentina and the UK, BBC reported.
His brother, Prince Harry, recently completed helicopter pilot training on Apache gunships, which are used by the Army Air Corps.