Testifying before the House Judiciary Committee, Mukasey said allegations the department had been politicized have been and continue to be addressed.
"It is absolutely crucial that the American people have complete confidence in the propriety of what we do, and I will work to make certain they can have such confidence," Mukasey said.
The attorney general also said tensions between the Democratically-controlled Congress and the executive branch are "part of the genius of the design of our Constitution."
With the end of the Bush administration fast approaching, Mukasey said the Justice Department is deep into planning for the transition to a new administration with an eye toward making the transfer of national security issues as seamless as possible.
Justice, he said, also is trying to make sure the November elections will take place with few problems.