Brock Long, the administrator of the Federal Emergency Management Agency (FEMA), announced his resignation Wednesday, calling his nearly two-year tenure the "opportunity of the lifetime." In a statement, Long said he is leaving to return home to his family. Long added the agency is "in good hands," with deputy Peter Gaynor taking over as acting administrator.

"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," said Long.

In a letter to FEMA employees, Long said stepping down was "one of the toughest decisions I have ever had to make."

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Secretary of Homeland Security Kirstjen Nielsen said Long "admirably led the men and women of FEMA during very difficult, historic and complex times." FEMA is part of the Department of Homeland Security (DHS).

"I appreciate his tireless dedication to FEMA and his commitment to fostering a culture of preparedness across the nation," Nielsen said in a statement.

Long was confirmed by the Senate in June 2017 and oversaw FEMA's response to three major hurricanes — Harvey, Maria and Irma — during his time as administrator. The agency was sharply criticized in particular for its response to Maria, which devastated Puerto Rico and knocked out power for months.

In September 2018, a congressional committee and the DHS internal watchdog launched investigations in Long's possible misuse of government vehicles. The revelations came to light as Long was spearheading recovery efforts during a busy hurricane season.

FEMA Administrator Brock Long testifies at a congressional hearing in Washington, D.C., on Nov. 29, 2018. AP

Long told reporters he would "never intentionally run a program incorrectly."

"Bottom line is if we made mistakes in the way the program was run then we will work with the OIG to get those corrected. Doing something unethical is not part of my DNA and it's not a part of my track record in my whole entire career. We will work with the OIG to get anything corrected," he said, referring to the department's Office of the Inspector General.

Politico and the Wall Street Journal reported at the time that Nielsen had asked for Long's resignation, which Long disputed.

"I've never been asked to resign. Secretary Nielsen and I talk everyday, we have a very professional functional relationship," Long told "Face the Nation."

Nielsen eventually determined Long had used government vehicles without proper authorization, but said he would not lose his job over it.

The DHS Office of Inspector General's office of public affairs told CBS News Wednesday it was unaware of any pending investigations involving Long.

In his statement Wednesday, Long said both the president and Nielsen had been "extremely supportive of me, the FEMA workforce and our mission" during his two-year tenure.

Rep. Bennie Thompson, the chairman of the House Committee on Homeland Security, said he hopes the president finds a capable replacement quickly.

"I hope the administration will be forthcoming with Congress as to the reason for Mr. Long's abrupt departure," Thompson said in a statement. "I also hope that the president will quickly nominate a capable replacement who has proven track record of emergency management. The American public cannot afford a leadership gap at FEMA given the increasing devastation caused by natural disasters and after the inadequate federal response to Hurricane Maria in 2017."