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The head of the FBI is strongly denying claims his agency tried to cover up evidence related to "Operation Fast and Furious" and the murder of Border Patrol Agent Brian Terry.

"Let me start with adamantly rejecting the suggestion that the FBI would in any way cover up what happened in the tragic killing of Brian Terry," FBI Director Robert Mueller told a Senate panel Wednesday. "To the contrary, every available necessary resource has been put on that and similar investigations where we lose one of our own."

It's the latest in a broader back-and-forth over tactics used by investigators from the Bureau of Alcohol, Tobacco, Firearms and Explosives to target gun-runners in Arizona. Launched in late 2009, "Fast and Furious" was said to be designed to follow gun purchasers in hopes that suspects would lead them to the heads of Mexican cartels.

But high-powered weapons tied to the investigation ended up at crime scenes in Mexico and the United States, including at Terry's murder in December 2010.

Two months ago, Rep. Darrell Issa, R-Calif, chairman of the House Oversight and Government Reform Committee, appeared on a Sunday morning news show and noted that a now-public FBI ballistics report labeled two guns tied to "Fast and Furious" as "K2" and "K3," but "there's no 'Ticket 1.'"

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Issa wondered if that meant there was a third weapon found at the scene, adding that the FBI "has a history in some cases of working with felons and criminals and hiding their other crimes in order to keep an investigation going."

In response, the Justice Department disclosed that "K1" -- shorthand for "known item 1" -- was not listed on the FBI ballistics reports because it is a blood sample from Terry, not a firearm. Still, two weeks later, Issa and Sen. Charles Grassley, R-Iowa, ranking member on the Senate Judiciary Committee, sent a letter to Mueller asking whether the FBI believes a third weapon killed Terry and what steps the FBI is taking to locate any other weapons associated with the attack.

On Wednesday, Mueller weighed in for the first time on the latest inquiry. He said he was "familiar with the suggestion that there was a third gun at the scene ... but the fact of the matter is there were only two weapons found at the scene."

Speaking to Grassley's committee, Mueller promised the FBI "will bring to justice those persons who are in any way involved in the killing of Officer Brian Terry," noting that there has already been one arrest in the case and the investigation continues.

In the wake of the investigation, dozens of Republicans have called for Attorney General Eric Holder's resignation, many of them criticizing Holder for failing to know about the operation as head of the Justice Department. Grassley has suggested Holder had ample opportunity to learn about it.

In recent Senate hearings and media interviews, Grassley noted that in January -- the month after Terry was killed -- he handed Holder two letters mentioning "numerous allegations" from whistleblowers "that the ATF sanctioned the sale of hundreds of assault weapons to suspected straw purchasers" and "two of the weapons were then allegedly used in a firefight … killing CBP Agent Brian Terry."

The letters, addressed to then-ATF head Ken Melson, did not cite "Fast and Furious" by name.

In addition, Grassley has cited several memos addressed to Holder in July and August 2010 that do mention the gunrunning investigation by name but no information about the operation's tactics.

Holder has said his office typically receives more than 100 pages of "so-called 'weekly reports' that, while addressed to me, actually are provided to and reviewed by" his staff and the deputy attorney general's staff. He said he does not "and cannot read them cover-to-cover."

In an exclusive interview with Fox News' Megyn Kelly, former Attorney General Alberto Gonzales said he "absolutely" agreed with Holder's assertion, and believes his claims are valid.

"There are multiple issues, multiple memos flowing up to the Office of the Attorney General every day. Sometimes you actually don't get to see them," Gonzales said. "And the fact that a memo is addressed to the attorney general doesn't mean that he actually saw it."

Gonzales, who served under George W. Bush, said it could be "like any other" government agency "where the top official just simply is unaware of" some operations, "not because he is out to lunch but simply because there are so many competing interests."

During recent hearings on Capitol Hill, Holder and Democratic lawmakers have repeatedly cited investigations in 2006 and 2007, including "Operation Wide Reciver," that lost track of hundreds of guns as a result of alleged "gun-walking."

Gonzales, who resigned as attorney general in mid-2007 after enduring his own political scandal over the firing of several U.S. attorneys, said he doesn't remember much about "Wide Receiver" or similar operations from his time leading the Justice Department.

"I'm very much aware of the fact that President Bush asked us to look to see what we could do -- what measures could be taken -- working with the Mexican authorities to stop the flow of guns from the United States illegally into Mexico," Gonzales said. But, he said, "I don't remember the specifics of this operation that people are alluding to."

As for whether Holder ends up resigning, Gonzales said he believes the current attorney general will stay until the end of President Obama's first term, even though he is likely "tired of this scrutiny" and "tired of these attacks."

"I think he knew, as I did, that you step into these jobs and it's hard," Gonzales said. "The attorney general is always involved in the most difficult, the most controversial issues, and that's just the way it is. And ... if you can't stand the scrutiny and if you are afraid of making a mistake, then you shouldn't be doing this job."

As for Mueller's remarks Wednesday, it's unclear if his latest comments will put to rest questions over how many guns were recovered at the scene of Terry's murder.

An ATF "briefing paper" about the murder, obtained by Fox News and sent to top Justice Department officials in Washington two days after the incident, said that "during the search of the area two ... AK-47 rifles, serial numbers 1983AH3977 and 1971CZ3775 were recovered near the scene of the shooting."

But emails in the hours after the incident show at least some ATF officials wondered whether a third gun had been recovered.

In one email, deputy ATF-Phoenix director George Gillett asks if two AK-47 rifles cited were "in addition to the gun already recovered this morning." It's unclear whether anyone responded to him.

Since then, some sources have accused the FBI of covering up evidence to protect an informant working inside a major Mexican cartel. That informant, sources have alleged, helped pay for the weapons used in the attack that killed Terry.

In addition, in recently disclosed recordings, a lead ATF investigator can be heard telling a Phoenix-area gun-dealer that an "SKS assault rifle out of Texas" had been found at the Terry murder scene.

In September, a spokeswoman for Grassley, R-Iowa, told Fox News it was "pretty clear" the ATF agent was talking about the Terry murder. Still, weapons involved in another case not tied to "Fast and Furious" -- the murder of Immigration and Customs Enforcement agent Jaime Zapata in Mexico -- were traced to Texas.