Attorney General Eric H. Holder Jr. clashed with congressional Republicans on Thursday, defending the Justice Department in the face of criticism of its “Fast and Furious” gun-trafficking sting and its refusal to turn over documents on the health-care law adopted last year.

Under exhaustive questioning from the House Judiciary Committee, Holder reiterated that his department would not provide Congress with more information about Supreme Court Justice Elena Kagan’s health-care-related role when she was President Obama’s solicitor general. Republicans are seeking internal e-mails and other documents, arguing that Kagan might have to recuse herself from the court’s decision on the health-care law if she was involved in the legislation.

Holder also was grilled over the Phoenix-based Fast and Furious operation, in which federal agents targeting drug cartels allowed guns to flow illegally onto U.S. streets and into Mexico. The operation led to a storm of criticism from Republicans, many of whom have urged Holder to resign.

The attorney general, who has resisted calls to step down, said the controversial Fast and Furious tactic known as “gun walking,’’ was “wholly unacceptable” and “must never happen again.” But he also condemned his accusers, saying the congressional investigation of the gun sting has been political and calling for cooperation in fighting firearms trafficking along the southwest border.

“Each of us have a duty to act, and to rise above partisan divisions and politically motivated ‘gotcha’ games,’’ Holder said. “The American people deserve better.’’

Holder began his remarks by asserting that his department has made “historic progress” in fighting terrorism and violent crime and protecting civil rights. But he immediately faced criticism from the committee chairman, Lamar Smith (R-Tex.), over his handling of requests for information about Kagan. Republicans have been stepping up the pressure on Kagan to take herself out of the health-care case. The high court recently announced it would review the law’s constitutionality.

Liberal groups have called on Supreme Court Justice Clarence Thomas to recuse himself from the health-care case, citing his wife Virginia’s involvement in conservative causes. But neither Kagan nor Thomas appears to be considering sitting out the term’s biggest decision.

As solicitor general, Kagan was the government’s top appellate lawyer. At her confirmation hearings, she said she played no role in preparing for the inevitable legal challenges to the health-care law.

But Republicans have said e-mails released to conservative groups under public records requests raise questions about the White House’s contention that Kagan had been “walled off” from discussions about the health-care act. In July, Smith began requesting internal Justice Department documents to determine Kagan’s involvement.

In an Oct. 27 reply, Assistant Attorney General Ronald Weich rejected the request, calling it “an unseemly encroachment on the judicial branch of government” and saying officials know of no information that contradicts Kagan’s statements in her confirmation hearings.

Holder reiterated that position Thursday, saying that giving Congress internal materials about someone who is now a Supreme Court justice would raise “separation of powers” questions. He said he does not recall Kagan being present for discussions about the health-care bill. “Each justice has to make these decisions,’’ he said.

Smith insisted that Congress is entitled to the documents. “The NFL would not allow a team to officiate its own game,’’ he said. “If Justice Kagan was part of the administration’s team that put the health-care mandate into play, she should not officiate when it comes before the Supreme Court.’’

Todd D. Peterson, a former high-level Justice Department official who is now a law professor at George Washington University, said the dispute is common in Washington and that the department typically refuses to provide sensitive internal material to congressional committees.

“Usually, this is resolved through some sort of compromise,’’ he said. “It’s in public this time because of the importance of the health-care litigation and the involvement of a Supreme Court justice.’’