The FBI said the Boston division assisted the military in a training exercise "to simulate a situation their personnel might encounter in a deployed environment" around 10 pm on Tuesday.
"Based on false information, they were mistakenly sent to the wrong room and detained another person and not the intended role player," the FBI said.
"First of all, we would like to express our deepest apologies to the person affected by the training exercise," Lieutenant Colonel Mike Burns, U.S. Army Special Operations Command, told CNN.
Burns stated that the drill was aimed at "improving the soldiers' ability to serve in realistic and unconventional environments", adding that the incident is under investigation. The FBI said no one was hurt.
According to the Boston Police Department, the incident occurred at the Revere Hotel Boston Common.
Local media reports indicated that the person found in the hotel room and detained by federal law enforcement was a Delta Air Lines employee.
The Atlanta-based airline told CNN it was investigating "the alleged incident in Boston that may have involved Delta employees."
