Weapons were unloaded from the Royal Navy submarine HMS Ambush yesterday.
The Gibraltar Port Authority had put in place a 200m maritime exclusion zone while the delicate operation was conducted over two days.
The nuclear powered submarine remains berthed alongside the South Mole following a collision with a merchant ship last week.
It sustained external damage to its conning tower but there was no impact on its nuclear reactor and the vessel is safe, according to the Ministry of Defence.
Royal Navy technicians are assessing the damage and have yet to decide whether the vessel will be repaired here or elsewhere.
A Royal Navy spokesman told the UK’s Press Association: “Some external damage was sustained by the submarine, and the extent is being investigated.”
“We are not prepared to give specific details, but the submarine is absolutely safe.”
“Comprehensive checks of HMS Ambush have shown that her reactor remains completely safe and there hasn’t been any increase in radiation as a result of this incident.”
The submarine will leave Gibraltar “as soon as the current work package is complete”.
The vessel was visited by Chief Minister Fabian Picardo yesterday afternoon.
Mr Picardo later tweeted about the visit.
Great to be aboard HMS Ambush today to see damage & personally thank her crew for their work & extend our welcome to Gibraltar @RoyalNavy
— Fabian Picardo (@FabianPicardo) July 27, 2016
Yesterday Spanish environmental group Agaden called on Spain’s acting Foreign Minister, José Manuel García-Margallo, to insist “robustly and energetically” that the UK repair the submarine elsewhere.