Rear Adm Kan said Rear Adm Winai Klomin, commander of the Naval Special Warfare Command (NSWC), had also been ordered to investigate and report back to the navy chief on whether the three officers had acted outside their line of duty.
If found guilty, they would be subject to both legal and disciplinary action, Rear Adm Kan said.
He said, however, that an initial investigation showed the three officers were carrying out an assignment for the Office of the Narcotics Control Board. They each carried a card showing they had undergone ONCB training and they were mingling with the protesters in Bangkok to follow drug suspects from Sattahip district of Chon Buri province.
Rear Adm Kan said he had tried to contact Rear Adm Winai for confirmation, but could not reach him.
It was earlier reported that Rear Adm Winai went to Nang Loeng police station to show police a document confirming that the three men were on assignment, investigating a drug case. The weapons were for self defence and the VIP passes of the Student and People's Network for Thailand's Reform (SPNRT) found on them were to facilitate their travel.
Adm Picharn Thiranet, commander of the Royal Fleet said this matter must be further investigated because the navy had never ordered any of its personnel to join a protest by any side.
The navy has never ordered its personnel to go to a protest site. It is not their duty," he said, adding that Rear Adm Winai would be able to explain this matter.
The men were detained at a road checkpoint in Bangkok after police found three pistols, ammunition, a bullet proof vest and other items in their vehicle, which also had false number plates. Official navy SEALs plates were found inside the vehicle, reports said.