It is understood the member of 45 Commando, based at RM Condor in Angus, claims he was assaulted by fellow marines.
Ministry of Defence police are investigating the allegation made by the 20-year-old to Tayside Police.
Commanding Officer Lieutenant Colonel Oliver Lee said: "I am aware that a marine from 45 Commando made a complaint to Tayside Police last week.
"The alleged incident is now under investigation by the MoD police, and together we are determined to get to the bottom of it.
"I have an absolute zero tolerance policy to indiscipline or unacceptable behaviour in 45 Commando."
A Tayside Police spokesman said: "We can confirm that a 20-year-old man attended at Arbroath police station at about 9.20pm on Wednesday June 23 and made a complaint, which was subsequently referred to the MoD."