President Bush stepped into the Justice Department's constitutional confrontation with Congress on Thursday and ordered that documents seized in an FBI search of a congressman's office be sealed for 45 days.

"The Department of Justice's search was part of an important investigation of alleged public corruption. At the same time, the bipartisan leadership of the House of Representatives believe the search violated the constitutional principle of separation of powers and the speech and debate clause of the Constitution," according to the president's statement.

"I recognize these are deeply held views," the president's statement reads. "So today I am directing the Department of Justice to seal all materials recovered from Congressman [William] Jefferson's office for the next 45 days, and not to allow access to anyone involved in the investigation."

The FBI searched Jefferson's office last weekend in the ongoing investigation into allegations that the Louisiana Democrat took bribes in exchange for helping a telecommunications company get favorable treatment in African business deals. Two men have entered guilty pleas in the case already, but Jefferson has not been charged with a crime.

The president ordered that the Justice Department inspector general will have the documents under his control for the time being.

"Our government has not faced such a dilemma in more than two centuries," the president said. "Yet after days of discussions, it is clear these differences will require more time to be worked out."

House Speaker Dennis Hastert, who has strongly criticized the administration's handling of the search as an intrusion on constitutional separation of powers, said the president's move is a step in the right direction.

"I think this is a good process for us to step back, negotiate with the Department of Justice, make sure that both the principles of the Constitution are upheld and that justice can move forward ... . I think it's an agreement we can move forward on," Hastert said.

Hastert later said there could be any number of private documents in a congressman's office, and he hoped that Congress and the administration could work out a protocol in the future.

"Today, we are directing the House Counsel to begin negotiations with the Department of Justice regarding the protocols and procedures to be followed in connection with evidence of criminal conduct that might exist in the offices of Members," according to a joint statement released by Hastert and House Minority Leader Nancy Pelosi.

Jefferson also said he believed the president's decision was "a step in the right direction."

"I think the president is starting down the road to make the correct decision. There's probably more could be done to truly correct this, which I think would involve returning the documents to the office, offices, from which they were taken. But I think this is a step in the right direction," Jefferson said, although he said he hadn't seen the president's release yet.

Some lawmakers have warned of a voter backlash against members of Congress "trying to protect their own" if party leaders keep escalating a constitutional dispute over the FBI's search of Jefferson's office.

Not long after Hastert and Pelosi demanded on Wednesday the FBI return documents it took, White House aides were in talks with Hastert's staff about the possible transfer of the material, perhaps to the House ethics committee, according to several Republican officials.

The goals of any transfer, they said, would be to deny the documents both to prosecutors and to Jefferson, a Louisiana Democrat ensnared in a bribery investigation, until the legal issues surrounding the weekend search of his office are resolved. The officials spoke on condition of anonymity, citing the confidential nature of the discussions.

In the meantime, House Judiciary Committee chairman, GOP Rep. James Sensenbrenner of Wisconsin, announced a hearing next week, "Reckless Justice: Did the Saturday Night Raid of Congress Trample the Constitution?"

But the confrontational approach by Hastert, R-Ill., and Pelosi, D-Calif., did not sit well with some colleagues.

"Criticizing the executive and judicial branches of our government for fully investigating a member of Congress suspected of criminal wrongdoing sends the wrong message and reflects poorly upon all of Congress," Rep. Barbara Cubin, R-Wyo., said in a statement. "They should not expect their congressional offices to be treated as a safe haven."

A GOP colleague, Sen. David Vitter of Louisiana, said the public "will come to one conclusion: that congressional leaders are trying to protect their own from valid investigations."

Vitter released a letter to his own GOP Senate leaders asking them to stop saying that the FBI raid violated the Constitution.

"For congressional leaders to make these self-serving arguments in the midst of serious scandals in Congress only further erodes the faith and confidence of the American people," Vitter wrote.

While some lawmakers contended the executive branch overstepped its authority, Senate Minority Leader Harry Reid of Nevada has declined to condemn the search.

"I'm not going to beat up on the FBI," said Reid, a frequent critic of the White House's use of executive power.

Their voices were in the minority on Capitol Hill in the wake of the 15-hour search during which agents collected evidence against Jefferson, an eight-term Democrat.

Historians said it was the first such search of a congressman's quarters in the more than two centuries since the first Congress convened.

Deputy Attorney General Paul McNulty said the raid was lawful and necessary. Justice Department officials have said Jefferson had refused to cooperate with the investigation.

The White House continued to try to keep its distance publicly. "We acknowledge the constitutional concerns of the House of Representatives and we also acknowledge the law enforcement obligations of the executive branch," White House press secretary Tony Snow said. "We hope that the two sides are going to be able to work this out."

In their rare joint statement, Hastert and Pelosi demanded that the FBI return the documents and that Jefferson then would have to cooperate with the investigation.

As evidence of Pelosi's lack of support for her fellow Democrat, she said he should step down from the powerful House Ways and Means Committee.

Jefferson filed a motion Wednesday asking the judge who signed the search warrant to force the FBI to return the seized items.

The congressman has refused to step down from the tax-writing committee and has acknowledged no wrongdoing.

Pelosi's curt letter to Jefferson, and the public nature of it, has riled a sizable bloc of her House troops — the 42-member Congressional Black Caucus. At private meetings with and without Pelosi on Wednesday, members of the group grew emotional and complained that Jefferson was being singled out.

The pointed out that another member under investigation, Rep. Alan Mollohan, D-W.Va., was forced to step aside as ranking member of the Ethics Committee but allowed to keep his seat on the Appropriations Committee.

"I have an excellent relationship with most" members of the CDC, Pelosi told reporters Thursday.

FOXNews.com's Greg Simmons and The Associated Press contributed to this report.