A Marine Accident Investigation Branch report has heavily criticised the Royal Navy for failing to implement lessons learned from the sinking of fishing trawlers.
It follows an 18 month investigation into the near sinking of the Karen in April 2015 in which the Northern Irish trawler's nets were snagged by a submarine.
The boat's four crew escaped unharmed after managing to release their equipment as the vessel was pulled heavily to port and its stern submerged.
The report found the submarine's commanders were unaware of the collision until three hours later.
Steve Clinch, Chief Inspector of marine accidents, said: "Eighteen months ago, the actions of the command team of a Royal Navy submarine placed the lives of the crew of the trawler Karen in danger.
"Regrettably, the reluctance of the Royal Navy to fully engage in the subsequent investigation resulted in this report taking significantly longer to deliver than would normally be the case."
At the time of the incident, which left the Ardglass-based prawn trawler badly damaged, there was intense speculation that a Russian submarine had been to blame - in part because British government ministers had insisted that no Royal Navy submarines were involved.
It wasn't until September 2015 that the MoD admitted that one of its boats was to blame, then expressing deep regret about the entanglement and offering to pay compensation.
Responding to the Marine Accident Investigation's findings a Royal Navy spokesperson said: "We have expressed our regret and remain sorry for the incident and delay in confirming our involvement.
"We’ve revised our procedures to reduce the risk that such an incident could happen again. We're reviewing the report's recommendations and continue to work closely with the maritime community to maximise safety."
Speaking on the publication of his team's report Mr Clinch added: "The accident happened because of insufficient passage planning by the submarine's command team and their failure to follow guidance on fishing vessel avoidance. Had its trawl warps not parted, it is almost inevitable that Karen would have capsized and sunk; the collision also presented a very significant risk to the submarine."
"As a result, it is now important that the Royal Navy reviews its procedures and training for the safe conduct of dived submarine operations in the same vicinity as vessels engaged in fishing. By its actions, the Royal Navy also needs to rebuild trust with the fishing industry."
The MAIB report went on to say that: "Evidence of the collision on board the submarine was either not observed or misinterpreted. It said the accident occurred because the submarine's command team detected no noise of trawling."
"The submarine was at a depth where it could, if necessary, pass safely beneath a merchant vessel, therefore the command team would not have perceived any risk of collision; as a result, no avoiding action was taken.
"The submarine's command team had assessed that the majority of shipping contacts in the area were merchant vessels. However, most were actually trawlers; this was predictable and should have been identified as a significant risk to the safety of the submarine and other vessels when preparing the submarine's passage plan."
"Had the submarine's command team appreciated the high density of fishing vessels and then followed Royal Navy guidance on fishing vessel avoidance, the accident would have been avoided because the submarine would have been slowed down and returned to periscope depth when the density of shipping increased."