Mike Elston, chief of staff to Deputy Attorney General Paul McNulty, is the fifth Justice official to leave after being linked to the dismissals of the prosecutors.
The firings have led to congressional investigations, an internal Justice Department inquiry and calls on Capitol Hill for the resignation of Attorney General Alberto Gonzales.
Elston's resignation is effective at the end of next week. Reached Friday afternoon, he confirmed his plans to leave but declined further comment.
His departure — and that of other senior Justice aides — has been anticipated since McNulty announced his own resignation last month.
In a statement, McNulty said Elston served the Justice Department "with distinction for nearly eight years."
"With his breadth of trial and appellate service, I have no doubt he will continue to enjoy an outstanding legal career," McNulty said.
Elston is taking a job with a law firm in the Washington area, according to the statement.
As McNulty's top aide, Elston's duties included overseeing the government's 93 U.S. attorneys nationwide. He was closely involved in the firings of seven of the eight prosecutors who were dismissed in 2006. In addition to helping plan those firings, he called several of the U.S. attorneys afterward trying to quell the growing outcry.
At least four of the prosecutors Elston contacted said they felt threatened by his calls, which they interpreted as demands to stay quiet about why they were fired. Congress is investigating the firings, which Democrats believe were politically motivated.
Elston and his attorney, Bob Driscoll, said the phone calls were never meant to be threatening.
Statements released from the House Judiciary Committee painted a different picture.
"I believe that Elston was offering me a quid pro quo agreement: my silence in exchange for the attorney general's," wrote Paul Charlton, the former U.S. attorney in Nevada.
John McKay, former top prosecutor in Seattle, said he perceived a threat from Elston during his call. And Carol Lam, who was U.S. attorney in San Diego, said that "during one phone call, Michael Elston erroneously accused me of 'leaking' my dismissal to the press, and criticized me for talking to other dismissed U.S. attorneys."
A fourth former U.S. attorney, Bud Cummins in Little Rock, Ark., had made a similar accusation in an e-mail released in March.
After Cummins told The Washington Post that he was surprised to find out that a Karl Rove protégé had been tapped to take his job, he received a phone call from Elston which he characterized as threatening if Cummins should speak to the press again.
Following Cummins' testimony, Elston wrote to the Senate Judiciary Committee in February rebuking the suggestion that he had leaned on the attorneys to keep them quiet about the circumstances of their dismissals.
"I do not understand how anything that I said to him in our last conversation in mid-February could be construed as a threat of any kind, and I certainly had no intention leaving him with that impression," Elston wrote in the two-page letter.
Other aides who have resigned in the wake of the firings include former Gonzales chief of staff Kyle Sampson and White House liaison Monica M. Goodling. A fifth official, Mike Battle, who ran the Justice office that oversees the U.S. attorneys, left in March.
Elston has worked for the Justice Department since 1999, starting as a trial prosecutor in Illinois and moving to northern Virginia in 2002. McNulty was the U.S. attorney there and brought Elston with him to Justice Department headquarters in late 2005.