However, the timing of her move is raising many questions as it comes on the heels of a series of problems at the SBI.
"It's certainly very questionable with the timing," said Mitch Kokai with the John Locke Foundation.
Kokai is among the chorus of voices skeptical of the move by the attorney general.
"It looks as if the attorney general was embarrassed, because his SBI director was responding poorly to media inquiries about problems at the SBI," he said.
Kokai is referring to Pendergraft's answers to questions about policies and procedures at the SBI.
Two former assistant directors of the FBI have been looking into practices at the state crime lab since a ruling that a North Carolina man who served almost 17 years in prison for murder was innocent.
An SBI agent testified that not all lab results were provided to attorneys. Pendergraft later confirmed the practice existed before she took over the SBI.
However just last week, Pendergraft maintained there were no widespread problems at the SBI.
"After that case cropped up, one would have expected the SBI and any other agency to say, 'okay there was a mistake here, where was the mistake made and what did we do wrong,'" Kokai said.
But Cooper is vigorously defending Pendergraft and his decision to move her to the brand new position of senior deputy attorney general overseeing Medicaid fraud.
"I wanted to have a good person at the head of Medicaid fraud and that's what I've done," Cooper said.
Pendergraft will earn $113,000 a year --roughly what she makes now.
A spokesperson for Cooper tells ABC11 Eyewitness News that it is unclear where the money for the new position will come from. But Cooper says the position is needed, because the state budget nearly doubles the size of the Medicaid Fraud Control Unit.
"I want a person with legal experience and law enforcement experience to head that up," Copper said. "Robin Pendergraft is the person and I'll think she'll do a great job."
However, not everyone is convinced.
"It's shades of, 'you're doing a heck of a job brownie' situation that we remember from George Bush," Kokai said.
Cooper appointed Pendergraft to the SBI job in 2001.
The new SBI director is Greg McLeod, who has been legislative council at the Department of Justice for the past seven years.
Meanwhile on Friday, Cooper suspended the six-agent unit that analyzes bloodstain patterns in the state crime lab. An outside investigation of the crime lab led to Cooper's decision.
Cooper says he asked two former assistant FBI directors investigating the lab to review cases involving blood spatter analysis. He says investigators looked at the cases and agreed the program should be suspended until issues about the unit have been looked into.