The Justice Department said Thursday that Columbia University has agreed to pay $9.5 million to resolve allegations that it improperly charged the National Institutes of Health for facilities and administrative costs on more than 400 federal grants.

Prosecutors say the Ivy League school inflated the amount of money owed for use of facilities from July 2003 to June 2015. Universities are allowed to charge a higher rate for research conducted on campus to offset maintenance and operations expenses. Although Columbia faculty carried out federally sponsored research in buildings owned by the state of New York, entitling the school to a lower rate of reimbursement, the university applied the higher rate, according to the complaint.

“It is disturbing that Columbia University, a prestigious institution, would improperly seek excessive cost reimbursements from NIH,” said Scott J. Lampert, a special agent in the Office of the Inspector General’s Department of Health and Human Services, in a statement. “Money gained by such behavior deprives other research programs of funds that could yield life-altering new treatments.”

Officials at Columbia say the school “believed in good faith” that it was appropriate to apply the rate for research performed in municipal buildings located on Columbia’s medical center campus.

“Columbia openly and consistently disclosed the rate applied to these buildings in its grant applications,” Caroline Adelman, a spokeswoman for the school, said in a statement. “The government disagreed with the university’s approach and took the position that a lower indirect cost rate was appropriate.”

The federal government has been cracking down on researchers misusing grant money.

In November, the University of Florida paid out nearly $20 million to settle allegations that it overcharged the government for the salaries of its employees without documenting their contributions and that it inflated the cost of services performed by a contractor.

West Virginia’s Wheeling Jesuit University agreed in August to pay $2.3 million to settle claims that it misappropriated research grant funding for over a decade. Around the same time, the National Science Foundation ordered Northeastern University in Boston to pay back $2.7 million for nearly a decade of mismanaging grant money from the agency.