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FBI agents carrying out a training exercise at a hotel in Boston broke into the wrong room and detained an innocent man, the agency confirmed.

The FBI said it was "assisting" the Department of Defence in conducting a mock investigation on Tuesday night.

But agents then stormed into the wrong room and handcuffed a man who had no clue as to what was happening.

The man who was wrongly detained was a Delta Air Lines pilot, CBS Boston reports.

"Based on inaccurate information, they were mistakenly sent to the wrong room and detained an individual, not the intended role player," the FBI said in a statement. "Thankfully, nobody was injured."

In the mix-up at the Revere Hotel, agents reportedly interrogated the man for almost an hour before realising their mistake. He had been asleep when the agents raided the room and at one point was pushed into the shower.

Police were called and confirmed that it was indeed a training exercise, the FBI said.

"Safety is always a priority of the FBI, and our law enforcement partners, and we take these incidents very seriously," the FBI said, adding it was reviewing the incident.