"It has been a great honor to serve our country as FEMA Administrator for the past two years".
Long was under investigation by the Homeland Security Department's watchdog, and word of it leaked just as Hurricane Florence struck last fall.
Nielsen said Long would pay back the taxpayer money spent to use government vehicles for those non-official trips, CNN.com reported.More news: North Atlantic Treaty Organisation won't station more nuclear missiles in Europe despite threat from Russian Federation
Long was widely praised for his tenure at a time when the United States faced its most devastating stretch of natural disasters since Hurricane Katrina in 2005.
In a statement announcing his resignation, Long said in part, "this has been the opportunity of the lifetime, it is time for me to go home..."
"Over the last two years, Administrator Long has admirably led the men and women of FEMA during very hard, historic and complex times", Nielsen said in a statement.
Two months after Long took over FEMA in June 2017, Hurricane Harvey dumped a record amount of rainfall in Texas and Hurricane Irma became one of the strongest Atlantic hurricanes on record before slamming into Florida.More news: Tip-in at buzzer lifts No. 19 LSU past No. 5 Kentucky
Long was criticized for the administration's disastrous response to Hurricane Maria in Puerto Rico, and for his refusal to correct President Donald Trump's false conspiracy theory that Maria's large fatality count on the island was fabricated by Democrats.
FEMA was criticized for its response to Puerto Rico's Hurricane Maria, in particular, a storm that resulted in almost 3,000 deaths. "We've got to figure out how to build better baseline capabilities at all levels of government".
Long, who served as the head of the agency through 220 disaster declarations, did not say when his final day will be, but once he officially leaves the position, Peter Gaynor will be named the acting administrator, the release also said. It was not immediately clear when he would leave the agency.More news: Assassin’s Creed III Remastered for Switch now listed on Ubisoft’s website