Yale has agreed to pay $7.6 million for allegedly making false claims on federal research grants, the U.S. Attorney’s Office in New Haven said Dec. 23, concluding a two-year investigation of Yale’s grant administration.

The investigation, which began in 2006, looked into 6,000 grants worth a collective $3 billion from 30 federal agencies — including the Department of Health and Human Services, the Department of Defense, and the National Aeronautics and Space Administration — between January 2000 and December 2006.

Prosecutors accused Yale of breaking the law by mishandling federal grants in two ways. First, some Yale researchers were said to have improperly transferred grant funds to accounts that were not specifically related to the purpose of the grant. Second, the government alleged that some researchers paid themselves for all their summer work, even time and effort unrelated to the grant.

The $7.6 million settlement is half actual damages and half penalties for the false claims, the U.S. Attorney’s Office said.

“This settlement sends a clear message that the regulations applicable to federally-funded research grants must be strictly adhered to,” Acting U.S. Attorney Nora Dannehy said in a statement.

A spokesman for the U.S. Attorney’s Office, Tom Carson, declined to comment on the origin of the investigation.

In a statement Dec. 23, the University acknowledged that some errors did occur, particularly with the transfers of funds between individual grant accounts. As part of the settlement, Yale denied liability for the false claims and was cleared of any wrongdoing. The government will not sue the University, the U.S. Attorney’s Office said.

The University said in the statement that it cooperated fully with the investigation. In response to the investigation, the Yale Corporation, the University’s highest governing body, began to require regular reports on research compliance in 2006.

In 2006, the University chartered the Office of Research Administration, which developed mandatory training courses for faculty and staff, reviewed policies, introduced a Web-based reporting system and stiffened oversight of fund transfers between grants. The office then established a committee to oversee audit, internal control and compliance issues.

Andrew Rudczynski, who oversees grants and contracts as Yale’s associate vice president for research administration, declined to comment.

The thicket of subpoenas, audits and new compliance policies was a source of strain and sometimes a point of contention between faculty members and administrators, who sometimes tended to blame each other for faults that arose in the grant accounting process.

“I recognize that this investigation has been stressful for many members of our faculty and staff, and I also recognize that federal regulations are sometimes burdensome,” University President Richard Levin said in a letter to faculty and staff Dec. 23. “We are doing our part to make the regulations more clear and compliance less burdensome.”

Some of the University’s reform efforts frustrated faculty. At a faculty meeting in February 2007, some science professors complained that the administration infringed on privacy and academic freedom by copying professors’ hard drives and requiring faculty members to undergo mandatory training.

Joel Rosenbaum, a biology professor who refused to surrender his hard drive and refused to attend the training courses, said researchers should focus on research, not bureaucracy.

Rosenbaum said the newly hired compliance officers should take responsibility for grant accounting rather than burdening professors. Grants include funds called overhead, which pay the host university for the use of its facilities and other administrative expenses such as accounting.

“I think it’s demeaning for faculty, who spend months writing grants and bringing in millions in overhead, to spend even more time attending class to become good grant accountants and financial secretaries,” he said in a phone interview.

Administering grants has also been difficult because of a poor software database to keep track of accounts, Rosenbaum said. The University said it is currently overhauling its online system for grant administration.

Robert Kenney, an attorney at Hogan & Hartson, the Washington law firm that represented Yale, declined to comment.

Income from grants and contracts, about $400 million annually, accounts for about a quarter of Yale’s operating budget.