James Walker Morales, 34, was taken into custody in New York late Wednesday night.
The break-in and thefts occurred between 6 p.m. on Saturday and 1 a.m. on Sunday, according to Worcester City Manager Edward Augustus, Jr.
Descriptions of the missing weapons were entered into the National Crime Information Center, an online database searchable by law enforcement.
Firefighters and police responded to the building after an employee called and reported smoke and signs of a break-in.
Morales was tied to the theft through blood left at the scene and through an electronic monitoring bracelet that he was wearing at the time because he is out on bail on a child rape charge. The bracelet places Morales “directly inside” the facility, the FBI said.
Morales had last been at the Worcester facility last Thursday to obtain copies of his discharge papers. The FBI did not provide any additional information on his service and did not say whether the guns had been recovered.
Morales is scheduled to appear in federal court in New York on Thursday to face charges of unlawful possession of a machine gun, unlawful possession of stolen firearms, and theft of government property. It could not immediately be determined if he has a lawyer.
The FBI has said that the theft is not related to terrorism.