DANNEMORA, N.Y. — A dozen employees at a northern New York prison have been suspended in connection with the investigation into the escape of convicted killers David Sweat and Richard Matt earlier this month, including the superintendent.

Assistant Commissioner for Correctional Facilities James O’Gorman has been put in charge of Clinton Correctional Facility, from which two inmates escaped on June 6, according to a statement from the State Department of Corrections and Community Supervision.

Superintendent Steve Racette and two other members of the executive team have also been placed on administrative leave, the release said. Nine others are on the security staff.

The three-week long hunt for Sweat and Matt came to a violent end over the weekend. Matt was shot and killed by a Border Patrol agent about 30 miles west of the prison on Friday, and Sweat was captured Sunday after being shot twice by a state police officer about 15 miles north of where Matt was killed. Sweat remains in Albany Medical Center, where his condition was upgraded to fair on Tuesday.

The State Inspector General’s Office, at the request of Gov. Andrew Cuomo, is investigating the escape.

A dozen Inspector General staff members, including detectives and experts with law-enforcement backgrounds, are involved in the probe at the prison, along with certified fraud examiners and computer forensic specialists, a source told The Press-Republican in Plattsburgh, N.Y.

Under the microscope, with employees being interviewed by investigators, are such prison records as personnel files, data from facility computers and the daily duties of staff and cell-block operation. The names of the other suspended employees were not released.

The 12 on administrative leave join Joyce Mitchell, a civilian employee who is jailed on charges of helping the inmates escape, and correction officer Gene Palmer, who faces felony charges connected with providing contraband to Matt and also destroying paintings, considered evidence in the case, given to him by the inmate.

Palmer is not accused of assisting the escape.