The deceased, Ibrahim Todashev, had been interviewed about his links to the bombing suspects before by the investigating agency and was shot after he attacked the agent, sources said.
An FBI special agent said the agent encountered Todashev while carrying out official duties. He said they were responding to the incident and still to have further details.
Three people, including an eight-year-old boy, were killed in the blasts while 280 were injured. Two young brothers, suspected to have carried out the attacks, later had an encounter with the police after shooting a police officer at the Massachusetts Institute of Technology campus and while the elder brother was killed, the younger was caught alive after a massive manhunt on April 19.