Joseph R. John, Sr. was given the interim job last October.
"Judge John is a skillful leader who is guiding the crime lab toward the highest standards," Cooper said in a news release. "I expect him to continue to make sure that the lab uses the latest science to pinpoint criminals and eliminate potential suspects."
The crime lab, which is part of the State Bureau of Investigation, came under fire last year when a report by independent investigators found that SBI agents helped prosecutors obtain convictions over a 16-year period by misrepresenting blood evidence and keeping critical notes from defense lawyers.
The SBI says John, a former judge, has made "significant improvements to ensure confidence in the lab’s work, including pursuing stringent new international standards."