WASHINGTON — The acting director of the Bureau of Alcohol, Tobacco, Firearms and Explosives and the U.S. attorney in Arizona resigned Tuesday amid investigations into a flawed law enforcement operation aimed at major gun-trafficking networks on the Southwest border, the Justice Department announced.

The operation, known as Fast and Furious, was designed to track small-time gun buyers at several Phoenix-area gun shops up the chain to make cases against major weapons traffickers. It was a response to long-standing criticism of ATF for concentrating on small-time gun violations and failing to attack the kingpins of weapons trafficking.

A congressional investigation of the program has turned up evidence that ATF lost track of many of the more than 2,000 guns linked to the operation. The Justice Department inspector general also is looking into the operation at the request of Attorney General Eric Holder.

Kenneth Melson will be replaced as ATF’s acting chief by B. Todd Jones, the U.S. attorney in Minnesota.

With Republicans in Congress and the department bickering over the investigation, Melson finally testified recently to Hill investigators in private. He said his department superiors “were doing more damage control than anything” and trying to keep the controversy away from top officials.

Also leaving was Dennis Burke, U.S. attorney in Arizona, whose office was deeply involved in Operation Fast and Furious. Burke will be replaced on an acting basis by his first assistant, Ann Scheel.

In a related change, the line prosecutor in the U.S. Attorney’s Office in Phoenix who worked on the Fast and Furious investigation, Emory Hurley, was reassigned from criminal cases to civil case work, according to an administration official, who spoke on condition of anonymity about the personnel matter.

The moves are the latest and most significant effort by the Justice Department to address the controversy. In earlier personnel changes, three ATF agents were laterally transferred starting in May from operational positions to administrative roles.

Jones will continue to serve as U.S. attorney when he assumes the top ATF spot on Wednesday. In a statement, Holder called Jones “a demonstrated leader who brings a wealth of experience to this position.”

In an interview, Jones said that ATF personnel “have been hugely distracted in some parts of the country with other things” and that he plans to listen to people within the agency, then “we’ll get everybody refocused, to the extent they are not focused.”

Melson will become senior adviser on forensic science in the Justice Department’s Office of Legal Policy, a development that brought an objection from Sen. John Cornyn, R-Texas. Instead of reassigning those responsible for Operation Fast and Furious, Holder should oust them, said Cornyn.

ATF intelligence analyst Lorren Leadmon testified before the House Oversight and Government Reform committee last month that of more than 2,000 weapons linked to Fast and Furious, some 1,400 have not been recovered.

Republican Rep. Darrell Issa of California, chair of the House panel, said in a statement that “the reckless disregard for safety that took place in Operation Fast and Furious certainly merits changes.”

Issa said his committee will pursue its investigation to ensure that “blame isn’t offloaded on just a few individuals for a matter that involved much higher levels of the Justice Department.”

Sen. Charles Grassley, R-Iowa, whose investigation brought problems with Operation Fast and Furious to light, called for a full accounting from the Justice Department as to “who knew what and when, so we can be sure that this ill-advised strategy never happens again.”

The strategy behind Fast and Furious carried the risk that its tracking dimension would be inadequate and some guns would wind up in the hands of criminals in Mexico or the U.S. and be used at crime scenes — which did happen to some of the guns.

Jones is a former military judge advocate as well as a prosecutor. Holder said, “I have great confidence that he will be a strong and steady influence guiding ATF in fulfilling its mission of combating violent crime by enforcing federal criminal laws.”

The attorney general said Melson brings decades of experience at the department and extensive knowledge in forensic science to his new role. Holder also praised Burke for demonstrating “an unwavering commitment” to the Justice Department and the U.S. attorney’s office, starting over a decade ago when he was a line prosecutor. Burke served as chief of staff to former Gov. Janet Napolitano, now U.S. Homeland Security Secretary and he was a top aide to Napolitano when she was Arizona attorney general.