The superintendent and 11 other workers have been put on leave at Clinton Correctional Facility after a pair of inmates escaped early this month, setting off a three-week-long manhunt, family members and New York state officials said on Tuesday.

The maximum security prison in Dannemora, New York, was at the center of a massive search for escaped murderers David Sweat and Richard Matt, who broke out on June 6 by cutting holes in the walls of their cells.

Sweat, 35, was wounded by police and taken into custody on Sunday. His condition was upgraded on Tuesday to fair, according to Albany Medical Center. Matt, 49, was shot and killed by police on Friday.

Three members of the executive team and nine security staff employees of the maximum-security facility were placed on administrative leave, the department announced on Tuesday. A department spokeswoman declined to identify any of the suspended employees by name or job title.

Superintendent Steven Racette was among the top officials at the prison placed on administrative leave, a women who identified herself as his wife told Reuters on Tuesday.

"He's been placed on administrative leave," said the woman who answered the phone at their Saranac Lake home. "We have no other comment."

The New York State Corrections Department said in a statement that state Assistant Commissioner for Correctional Facilities James O'Gorman would oversee the facility near the Canadian border "as the new leadership team transitions this week."

The episode has thrust Racette, who earns $132,040 as superintendent of Clinton, into the spotlight.

Investigators are examining conditions that allowed the two inmates to use smuggled tools to cut through their cell walls, climb along a catwalk, slither through a steam pipe and pop out a manhole outside the prison walls.

Two prison workers have been charged in connection with the escape - prison tailor shop supervisor Joyce Mitchell, 51, and corrections officer Gene Palmer, 57.

Racette has declined to be interviewed.

The son of a prison superintendent, Racette has worked in the prison system since 1979, when he started as a correction officer trainee, rising through the ranks to superintendent in 2010.

Clinton, New York's largest prison, is among 10 upstate prisons where Racette has worked.

The escape has triggered an investigation into Clinton by the state's inspector general, which has the authority to seize documents and question witnesses, including Racette.