"I regret the concerns this has raised regarding the use of taxpayer dollars," Tom Price said in a statement, a day after Trump issued a forceful public rebuke about his flights on private aircraft.
"Today, I will write a personal check to the US Treasury for the expenses of my travel on private charter planes."
In all, Price has flown on 26 separate trips this year on private aircraft, totaling some USD 400,000, according to Politico.
The trips were for government business, HHS said, but some of the flights were to destinations where Price owns property, or where he met relatives.
Asked if Price could be sacked, Trump on Wednesday said "we'll see," adding that he was "not happy about it."
In his statement, Price said he and his staff would continue to cooperate with the internal review.
"I will take no more private charter flights as secretary of HHS. No exceptions," he said.
Five Democratic lawmakers had called for Price's resignation.
US government guidelines call for traveling officials to take scheduled commercial flights whenever possible.
Price's two predecessors under president Barack Obama traveled almost exclusively on commercial flights, Politico reported.
"It is clear to me that in this case, I was not sensitive enough to my concern for the taxpayer," Price said. "I know as well as anyone that the American people want to know that their hard-earned dollars are being spent wisely by government officials."
Another Trump cabinet member, Environmental Protection Agency Administrator Scott Pruitt, has also come under scrutiny for violating travel policy.
The Washington Post revealed that since February, Pruitt traveled three times on private jets and once on a military aircraft, costing tax-payers some USD 58,000.
The EPA's Office of General Counsel gave advance legal authorization for each trip and said Pruitt flies commercial except in particular circumstances, the Post reported, citing documents provided by the agency.
In August, Treasury Secretary Steven Mnuchin, a wealthy former Wall Street banker and Hollywood producer, was pressured to justify use of a government plane to fly with his wife to Kentucky, where viewing for that day's total eclipse of the sun was ideal.
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