Politico, citing three people familiar with the matter, said the Department of Homeland Security's Office of Inspector General (OIG) was probing Long's use of official vehicles to travel between Washington and his home in North Carolina during his time as FEMA director.
Specifically, Long is accused of using government cars for personal weekend travel to his hometown of Hickory, North Carolina - which has drawn scrutiny from DHS Secretary Kirstjen Nielsen as well as the inspector general.
The investigation includes, but may not be limited to, travel using government resources, and that would include the administrator's travel in government vehicles on the taxpayer's dime, the source told CNN.
Several current and former Trump administration officials have been investigated over their travel expenses.
"I would never intentionally run a program incorrectly", Long continued.
Since his first days in the job, Long has used a staff driver to take him back to North Carolina on weekends.
Long has said he will cooperate with the investigation and take it as an opportunity to make improvements to remain in line with regulations.
"Doing something unethical is not part of my DNA and it's not part of my track record in my whole entire career", said Long, who leads the Federal Emergency Management Agency.
"What concerns me the most is trying to get to the people who didn't evacuate and that's incredibly hard to do, so we can't put our own people in danger", said administrator Brock Long, who spoke to CBS News right before he went to brief the president.
FEMA director of external affairs Jessica Nalepa said any questions regarding an investigation should be directed to the DHS IG, adding FEMA "fully cooperates with all investigations conducted by the DHS OIG".
Long did not respond to Politico's request for comment.
Politico said Long began using a staff driver for his trips home from Washington when his term began a year ago, and that aides also traveled with him at taxpayer expense.
The Department of Homeland Security's inspector general's office is reportedly looking into whether he misused taxpayer dollars. Veterans Affairs Secretary David Shulkin was sacked in March amid questionable travel charges and a growing rebellion in his agency about the privatization of medical care.