Former Marine Gen. John Allen speaks during a news conference at the Pentagon March 26, 2012. President Barack Obama says he has accepted Allen’s request to retire from military. (Haraz N. Ghanbari/AP)

The Pentagon has decided to keep secret the details of its investigation into Marine Gen. John R. Allen, the former commander of U.S. troops in Afghanistan, citing privacy concerns.

The Defense Department Office of the Inspector General formally denied a request from The Washington Post, filed under the Freedom of Information Act, to disclose records of its probe into Allen’s relationship with Jill Kelley, a Tampa socialite with whom he exchanged thousands of pages of e-mails and other documents.

The denial was dated Feb. 15, although it was not delivered to The Post until Monday. Defense Department officials said requests made by several other media organizations had also been rejected.

Allen announced last week that he would retire from the military, turning down an offer from President Obama to become NATO’s supreme military commander for Europe. Allen said he wanted to spend more time with his ailing wife after a 37-year career in the armed forces, including the last 19 months as commander in Afghanistan.

The e-mails came to light during an FBI investigation into other Kelley e-mails that revealed that former David H. Petraeus had an extramarital affair with his biographer. Petraeus resigned as CIA director in November.

The Pentagon inspector general’s office cleared Allen of wrongdoing last month after conducting an investigation at the request of Defense Secretary Leon E. Panetta. If he had not decided to retire, however, Allen probably would have faced renewed questions about his relationship with Kelley during his confirmation hearing for the NATO job.

The agency has not disclosed any details about its findings. In its denial letter to The Post, the inspector general’s office said that revealing any records related to the Allen probe would “constitute a clearly unwarranted invasion of personal privacy.”

Bridget Serchak, a spokeswoman for the inspector general’s office, said the agency generally does not release reports of probes into senior Pentagon officials unless investigators find evidence of misconduct.

Even then, the agency releases its findings only if requested to do so under the Freedom of Information Act, a process that can take months.

During the last fiscal year, the inspector general’s office substantiated misconduct complaints against 10 senior military officers and civilian leaders, according to a report submitted to Congress in December.