The Marine Accident and Investigation Branch (MAIB) is investigating the incident on Friday, involving the Banff-registered Reliance III - which previously featured on reality TV show Trawlermen.
The vessel was fishing east of Fair Isle when the alarm was raised at 5.10am.
The MAIB confirmed it was carrying out preliminary investigations into the "amputation of a crew member's limb on board a UK registered fishing vessel".
The chief of a fishing association said the quick thinking of the crew in administering first aid prevented the injured fisherman's condition from deteriorating. He was then airlifted to Aberdeen for further treatment.
Mike Park, Chief Executive of the Scottish Whitefish Producers' Association, said: "I have been in constant communication with the skipper and owner of the vessel. This was an unfortunate incident that led to a severe injury.
"The skipper and crew secured the patient's condition preventing him from deteriorating further until such times as he could receive medivac from the vessel.
"Fortunately, the prompt actions of those onboard addressed the situation at hand which means the seaman is now in hospital recovering safely."
The vessel was back fishing off Orkney on Monday, according to satellite trackers.
In 2022, Reliance III's skipper, John Clark, said he had invited camera crews filming BBC show Trawlermen on board during treacherous winter months at sea to show them "what fishing is really like and why it can be so dangerous".
Clark, who started fishing almost 40 years ago, is a director of the Reliance Fishing Company.
The Record approached the skipper for comment but did not receive a response.
A Coastguard spokesman said: "At 5.10am on Friday October 17, HM Coastguard received reports of a casualty with an arm injury aboard a vessel 45 nautical miles off Sumburgh, Scotland.
"An HM Coastguard Rescue Helicopter was sent, and the casualty was rescued to Aberdeen for onwards medical care.
"Lerwick Coastguard Rescue Team also attended to prepare a Helicopter Landing Site on shore."