Investigators believe the man had let the 100-foot vessel loose, WHDH-TV reported.
"The individual must have set the boat free," Fire Capt. Steve Waldron said.
"It was tied up to the pier and secured. Looks like he went through a lot of trouble to unhitch the lines and let it drift."
The man could face criminal charges. But police took him to Massachusetts General Hospital for examination.
Waldron said the ferry drifted about 400 yards in an area where sailboats and yachts were anchored and could have done a lot of damage. An onlooker in East Boston noticed the vessel was moving slowly on an erratic course and alerted police.
No injuries or serious damage to other boats or the ferry was reported.