Updated

House Republicans on Wednesday turned their sharp questioning over "Operation Fast and Furious" toward Homeland Security Secretary Janet Napolitano, who acknowledged her agents were twice told to "stand down" in deference to what she called a "very troublesome" operation.

Napolitano, at one point likening the questioning to a cross-examination, said repeatedly she only learned of "Fast and Furious" after Border Patrol Agent Brian Terry was killed in December. She emphasized the operation, conceived and run by the Bureau of Alcohol, Tobacco, Firearms and Explosives, "was an ATF operation," under the auspices of the Justice Department, not her department.

Still, during a hearing before the House Judiciary Committee, outspoken Republicans wanted to know why she didn't press for more answers in the wake of Terry's death, and they called on her to meet more regularly with her Justice Department counterparts, suggesting more frequent discussions could help prevent incidents like Terry's murder.

Napolitano said she has never spoken with Attorney General Eric Holder about "Fast and Furious," a revelation Republicans strongly criticized.

"There needs to be better communication, so somebody can say, 'Whoa! This is a crazy idea, you're giving guns to drug smugglers that are going to come back and be used?" said Rep. Bob Goodlatte, R-Va.

More On This...

    Holder, however, has said he was not aware of "Fast and Furious" -- or at least its controversial details -- until after concerns were raised publicly. And, in a letter to lawmakers three weeks ago, he said that while "some senior officials" within the department knew of an operation called "Fast and Furious," they "were not advised of the unacceptable operational tactics being used in it."

    Nevertheless, on Wednesday, Napolitano said one reason she hasn't spoken to Holder directly about "Fast and Furious" is that the Justice Department's inspector general is currently engaged in an investigation into the matter, and she said she wouldn't know details about "Fast and Furious" because it "was an ATF operation."

    Napolitano warned lawmakers not to "rush to judgment here," but she said there "will be lessons learned from this, and there very well may be changes in the field as a result of this."

    Launched in late 2009, "Fast and Furious" hoped to target major gun-runners in Arizona by following gun purchasers to senior-level officials within Mexican cartels. But high-powered weapons tied to the investigation ended up at crime scenes in Mexico and the United States, including that of Terry's murder.

    On Wednesday, Republicans tried to use their questioning of Napolitano, a former U.S attorney in Arizona, to bolster allegations that Justice Department officials knew details of "Fast and Furious" early on. Republicans have noted that, starting in at least March 2010, officials within the Justice Department's criminal division approved wiretaps as part of the investigation.

    During a lengthy back-and-forth, Napolitano acknowledged that wiretap applications are approved by the Justice Department and include a "summary" or "narrative" of the case. But when Rep. Trey Gowdy, R-S.C., tried to suggest it was "disingenuous" for the Justice Department to say officials didn't know about "Fast and Furious," Napolitano balked.

    "Someone at the Department of Justice had to know about 'Fast and Furious' for the [wiretaps] to ever have been approved, correct?" Gowdy asked Napolitano. "If there were [wiretaps] approved in 'Fast and Furious' -- and there were -- the Department of Justice would had to have known about it, correct?"

    Napolitano wouldn't comment, telling lawmakers she would "leave that for your own investigation."

    Rep. Darrell Issa, chairman of the House Oversight and Government Reform Committee, is leading a congressional investigation into "Fast and Furious." Republicans and Democrats have increasingly become divided over the direction of the probe.

    Issa told Napolitano he believes an Immigration and Customs Enforcement agent assigned to a "Fast and Furious" task force "likely was very aware that there was gun-walking going on."

    Napolitano said, with thousands of agents engaging in hundreds of operations under the DHS umbrella each day, information from "an agent assigned somewhere about some matter would not net necessarily come to ICE headquarters, much less DHS headquarters."

    Napolitano said that, since Issa launched his own investigation into "Fast and Furious," she has learned about two incidents in which ICE agents were told to "stand down" on their own investigations so ATF agents could continue with parts of "Fast and Furious."

    The incidents, in November and December 2009, spurred a meeting between ICE, an ATF official, and Assistant U.S. Attorney Emory Hurley, who led the "Fast and Furious" prosecution team. At the meeting, Hurley requested that ICE coordinate with ATF before taking any enforcement actions against targets that might be associated with "Fast and Furious," Fox News was told.

    As Napolitano put it, ICE was told "the ATF operation would take precedence." She said she is not aware of any other incidents where ICE ceased investigating at the behest of ATF.

    Meanwhile, Issa pressed Napolitano on why she didn't ask more questions about "Fast and Furious" in the three months after she learned of Terry's death, before Holder asked the Justice Department's inspector general to investigate.

    "Aren't you ... furious that the Justice Department -- not ATF -- the Justice Department withheld from you the knowledge of 'Fast and Furious' during this entire period of time, including one in which you had an agent dead?" Issa asked.

    Napolitano said everyone "should be outraged" at Terry's death.

    "The first thing is to recognize who actually killed him, and that our No. 1 priority was to make sure the shooters were found," she said. "As quickly as I could get to Arizona after his death, I met with the FBI, their agents in charge. I met with the [prosecutor] who was going to conduct that investigation, and that was my number one concern, that those responsible for the shooting death of Agent Terry were brought to justice. And that's what I was being kept apprised of."

    The chairman of the committee that welcomed Napolitano Wednesday, Rep. Lamar Smith, R-Texas, is calling for a special counsel to look into questions surrounding "Fast and Furious."

    After the hearing, Issa and Sen. Chuck Grassley, R-Iowa, distributed a letter they sent to Holder, looking for answers into the murder of ICE agent Jaime Zapata in Mexico early this year. In particular, they are seeking information on any surveillance conducted on suspects in the case and wondering why action wasn’t taken against suspects during what the lawmakers view as at least two opportunities.

    In a statement to news outlets, Issa and Grassley said they're concerned tactics "similar" to those of "Fast and Furious" could have played a role in Zapata's death.