The investigation into a controversial U.S. gun-trafficking investigation took an unexpected turn last weekend when the ATF head met secretly with congressional aides and conceded that his agency made mistakes in directing “Operation Fast and Furious,” officials said Wednesday.

Kenneth E. Melson, acting director of the Bureau of Alcohol, Tobacco, Firearms and Explosives, had been scheduled to speak to congressional investigators next Wednesday, in the presence of Justice Department and ATF lawyers. Instead, he brought his own attorney and was interviewed twice over the Fourth of July weekend.

Melson’s decision, which took ATF and Justice Department officials by surprise, was the latest fallout from the Fast and Furious sting. That now-defunct operation targeted Mexican gun traffickers, but it has been linked to the killing of a Border Patrol officer. Congressional Republicans have criticized ATF over the operation and are pushing to learn whether senior Justice Department officials were involved.

The transcript of Melson’s interview has not been publicly released, but people familiar with it said that the ATF leader indicated that Attorney General Eric H. Holder Jr. did not know about the operation, that it would be unusual for other Justice Department officials in Washington to know the details and that the U.S. attorney’s office in Phoenix was overseeing the program.

Yet the ATF chief also said he moved to reassign managers involved in Fast and Furious and became “sick to his stomach” upon learning “the full story” of the operation, according to a letter sent Tuesday to Holder by Rep. Darrell Issa (R-Calif.) and Sen. Charles E. Grassley (R-Iowa). They are leading the congressional probe.

Issa and Grassley added in their letter, released Wednesday, that Melson said that he and other ATF officials wanted to cooperate more with Congress but that the Justice Department, which oversees the agency, prevented that.

“ATF leadership appears to have been effectively muzzled while the DOJ sent over false denials and buried its head in the sand,” the lawmakers wrote. “That approach distorted the truth and obstructed our investigation.”

That triggered a sharp response from Assistant Attorney General Ronald Weich, who wrote in a letter to the two Republicans that the department has produced or made available for review more than 2,000 pages of documents. “Regrettably, your letter unfairly criticizes both the Department’s efforts to address the Committee’s concerns and the integrity of the professionals at the department who have worked long hours to make responsive information available to you,’’ Weich said Wednesday.

The Justice Department’s inspector general is investigating the allegations surrounding the operation. Robert Sherwood, a spokesman for the U.S. attorney’s office in Phoenix, said Wednesday, “The U.S. attorney’s office gives case-related legal advice to federal agencies, it doesn’t direct them. ATF agents and their tactical decisions are all supervised by ATF.”

Fast and Furious allowed the suspected illegal purchase of hundreds of semiautomatic firearms in Arizona gun shops so ATF agents could watch where the guns ended up, with the hope of bringing down a Mexican cartel. Under pressure to snag bigger players in trafficking organizations, ATF launched the operation in late 2009.

It has led to 20 indictments. But two of the AK-47s recovered near the scene of the fatal shooting of U.S. Border Patrol Agent Brian A. Terry in December were bought in Fast and Furious. And several ATF agents recently told Congress that they were ordered not to stop people they suspected of having the illegal guns.

Issa and Grassley said that Melson acknowledged ATF agents had witnessed the transfer of weapons from so-called straw purchasers to third parties without following the guns further.

Melson’s interviews, on Sunday and Monday, followed weeks of pressure on ATF’s leadership over Fast and Furious. Some news organizations have reported that Melson — a former federal prosecutor and longtime Justice Department official who moved to ATF in 2009 — would probably be ousted soon or resign over the operation.

But Issa and Grassley’s letter said that Melson has not been asked to resign, and law enforcement officials said Wednesday that they knew of no current efforts to remove him. One source who was present for Melson’s questioning said the agency leader came forward on his own because he thinks the Justice Department’s handling of the controversy has been “problematic” and was harming ATF.

Melson told investigators that it was only after the operation became controversial that he personally reviewed hundreds of documents in the case, Issa and Grassley said. Other information given to Congress indicates that Melson was briefed on Fast and Furious and asked questions about it, according to sources familiar with the material. But Melson denied that he knew the details.

Congressional investigators are also probing whether some of those suspected of gun trafficking in Fast and Furious were already known to the FBI and the Drug Enforcement Administration and may have been informants for those agencies.

Melson, when asked, told the investigators that that may be true and that he recently learned that other federal agencies may not have shared important information with ATF, Issa and Grassley said.

But it is unclear whether the FBI and DEA were involved with the suspects in the ATF operation and whether such involvement would have changed its outcome. On Wednesday, some federal law enforcement officials played down the possibility, which congressional investigators continue to explore.