WASHINGTON — Brock Long, the administrator of the Federal Emergency Management Agency who was praised for his agency’s response to Hurricane Harvey but sharply criticized for its handling of Hurricane Maria’s devastation of Puerto Rico, announced on Wednesday that he would resign.

Mr. Long’s tenure was also punctuated by a controversy that had nothing to do with storms. The inspector general at the Department of Homeland Security, which oversees FEMA, found in September that he had improperly used government vehicles to travel between work and his home in North Carolina, where his wife and two sons live.

In a statement announcing his departure, Mr. Long noted that in his two years leading the agency, FEMA had handled more than 220 declared disasters, including during several hurricanes that caused profound damage in Texas, in Puerto Rico and along the East Coast.

“While this has been the opportunity of the lifetime, it is time for me to go home to my family — my beautiful wife and two incredible boys,” he said. “As a career emergency management professional, I could not be prouder to have worked alongside the devoted, hardworking men and women of FEMA for the past two years.” The agency declined a request for an interview.