An investigation has been launched into the incident and the UK submarine will be undergoing further checks.
"At approximately 13:30 local time today, HMS AMBUSH, an Astute-class submarine, while submerged and conducting a training exercise was involved in a glancing collision with a merchant vessel off the coast of Gibraltar," the ministry said in a Wednesday statement.
The submarine suffered some external damage but the crew were not injured and the nuclear plant was not affected, according to the statement.
"We are in contact with the merchant vessel and initial indications are that it has not sustained damage."
