Authorities were probing the possible involvement of two army officers.
Judge Advocate General Gen Jira Komutpong insisted the stolen weapons were not involved with recent cases of political unrest or the military's recent raids to confiscate illegal weapons, and that only about 40 guns had been stolen, not 54 as reported earlier by the media.
All but two of the more than 40 stolen guns were from criminal cases the Bangkok Military Court has already ruled on, Gen Jira said.
Although the cases were closed, the court keeps weapons for a certain period in the event a case later needs to be re-investigated, he said.
"Those stolen weapons were not seized in National Council for Peace and Order (NCPO) operations, nor are they war weapons. All the stolen weapons are from criminal cases in which the culprits were military personnel," Gen Jira said.
Some of the cases involved relatively minor infractions, such as carrying weapons in public places without permission, while others included attempted murder, murder and money extortion cases, he said.
The Bangkok Military Court has assigned Lt Col Surawuth Sri-angkura, an officer with the court, to lodge a complaint with police seeking legal action against Capt Chinaphol Au-rungroj and Sgt Maj 1st Class Somkiat Mayong on suspicion of being involved with the missing weapons.
Capt Chinaphol, who was the court officer responsible for keeping the keys of the room where the seized weapons were stored, has already been detained, Gen Jira said.
He has been suspended pending an investigation.
The military has provided police with the personal information of SM 1 Somkiat, also a court officer, who is still at large. A warrant has been issued for his arrest.
The Judge Advocate General's Department has scheduled a news conference for today at which it is expected to officially inform the press of the weapons theft.
An informed source said the Bangkok Military Court had first discovered that a number of weapons had gone missing during a July 23 trial in an attempted murder case involving an automatic 9mm that was seized as evidence.
But when the judge ordered it to be brought out to show to the plaintiff to determine whether it was the one used in the crime, the gun was not there, the source said.
At another trial the next day, the court judge asked to see a .38 revolver seized in a murder case, the source said. It, too, was missing.
That was when Cap Chinaphol was detained for questioning. More weapons were later found to have gone missing.
NCPO spokesman Winthai Suwaree said the authorities were searching for the missing weapons while pursuing legal action against the suspects.
He echoed Gen Jira's statement that the stolen weapons were not ones that had been seized during the NCPO's weapon crackdowns.