Partners HealthCare Systems Inc. of Boston earned $84 million in its most recent fiscal quarter despite a large one-time expense for reimbursements to the federal government.

On an operating basis Partners posted a $12 million loss over the last three months of 2012, but offset that with gains from its investment portfolio and philanthropy to end the period positively.

However, the medical system absorbed a $76 million expense during the period for reimbursements to the Centers for Medicare and Medicaid Services. The charge was the result of federal Medicare policy — recouping a portion of payments made between 2010 and 2012 — that will affect all US hospitals, according to Partners, the parent company for Massachusetts General Hospital, Brigham and Woman’s Hospital, and other facilities.

“Providers are facing a great deal of pressure in the current health care environment — particularly from government payers,” said Peter K. Markell, the chief financial officer at Partners.

In the last quarter of 2011, Partners reported a net gain of $128 million and nonoperating income of $56 million.