The helicopter plunged into the sea as it approached Sumburgh airport on the southern tip of Shetland on Friday, killing three men and one woman.
The search for the data recorder had been described as challenging due to the "nature of the environment" where the wreckage was located.
A statement from the Air Accidents Investigation Branch (AAIB) said: "The combined voice and flight data recorder from the AS332 L2 Super Puma helicopter has been successfully recovered and will be transported to the AAIB HQ in Farnborough later today."
The AAIB said it had not identified the cause of the crash in a statement released earlier today.
Early indications show the flight approach of the AS332 L2 Super Puma was normal until three miles from the airport runway and it crashed into the sea two miles west of runway 09 when airspeed dropped along with an ''increased rate of descent'', the AAIB said.
''The evidence currently available suggests that the helicopter was intact and upright when it entered the water,'' a statement said.
''It then rapidly inverted and drifted northwards towards Garths Ness.
"The helicopter was largely broken up by repeated contact with the rocky shoreline.
''Some items of wreckage have already been recovered and will be transported to the AAIB's HQ in Farnborough."
It is hoped that the flight data recorder will shed light on what caused the helicopter to come down.
The AAIB said the investigation is at an early stage and the factors that led to the crash cannot yet be identified.
Representatives from the French accident investigation authority (BEA), the helicopter manufacturer and the engine manufacturer were also invited to join the investigation by the AAIB.
The Bibby Polaris salvage boat arrived at Lerwick harbour in Shetland carrying some of the wreckage at about 4am today, the harbour's port control has said.
John Henderson, managing director of marine engineering firm Ocean Kinetics, told STV News that divers had located further parts of the aircraft.
''Ocean Kinetics have successfully located, lifted and passed the gearbox and rotor head of the helicopter to the Bibby Polaris, who took the parts on board,'' he said.
''We have also located both engines and parts of the cockpit, which will likely be recovered on Thursday.''
The industry's helicopter safety steering group (HSSG) has been reviewing the suspension of Super Puma flights introduced after the crash.
Representatives from operators, trade unions and regulators gathered in Aberdeen today to discuss the issue after a meeting on Wednesday failed to reach a decision on when the helicopters could return to the skies.
CHC has temporarily suspended all flights of the three types of Super Puma helicopter that it operates - the L, L2 and EC225.
Fellow operators Bond Offshore Helicopters and Bristow also enforced a temporary suspension of all Super Puma flights except emergency rescue missions in the wake of a recommendation by the HSSG.
The freeze on using the helicopter type is causing disruption to the movement of workers both on and offshore.
The Super Puma is said to make up about half of the UK offshore industry's 75-strong helicopter fleet. Different aircraft models and alternative methods of transport, such as boats, are being used or looked at to transport people on and off North Sea platforms.
Union officials have said that the return of Super Pumas to the skies cannot be backed until the cause of the crash is known.
The Super Puma was travelling from the Borgsten Dolphin support vessel when it came down with 16 passengers and two crew on board.
The victims have been named as Duncan Munro, 46, from Bishop Auckland, County Durham; George Allison, 57, from Winchester, Hampshire; Sarah Darnley, 45, from Elgin, Moray; and 59-year-old Gary McCrossan, from Inverness.
A support centre set up by Aberdeen City Council for people affected by the crash will be open seven days a week for three weeks from today.
Friday's crash was the fifth incident involving Super Pumas in the North Sea since 2009.
In April 2009 an AS332 L2, operated by Bond, went down north east of Peterhead on its return from a BP platform, killing all 14 passengers and two crew on board. A fatal accident inquiry into the 2009 crash is expected to begin in Aberdeen next January.