The House of Representatives and the Justice Department are in negotiations over new protocols and procedures for law enforcement searches of Congressional offices — talks that began in the wake of the controversial May 2006 raid on Rep. William Jefferson’s (D-La.) Capitol Hill office.

An appeals court has ruled that raid was unconstitutional and the Supreme Court on Monday refused a Justice Department request to reconsider that ruling.

According to House General Counsel Irv Nathan, discussions between the House and DOJ are in “preliminary” stages, but “we have put forward concrete proposals.” Nathan said the goal of the discussions — led by his office and by Assistant Attorney General Alice Fisher — is to produce “either a set of procedures, a memorandum of understanding or perhaps legislation, that would make clear the rules for law enforcement actions in Congressional offices.” Nathan would not set a timetable for the talks, but said he hoped a resolution could be reached this year.

In February testimony before the House Judiciary Committee, Attorney General Michael Mukasey hinted at these discussions, saying that despite the DOJ appeal to the Supreme Court, “we would much prefer to resolve that case in the way that most disputes with respect to privilege and other matters are resolved between Congress and the Justice Department, namely by conversation and accommodation. And, as I understand it, that’s actively under way.”

The Supreme Court decision Monday leaves in place a U.S. Court of Appeals for the District of Columbia Circuit decision that the Justice Department violated the Speech or Debate Clause by reviewing documents in Jefferson’s Congressional office without giving him the opportunity to first assert privilege over documents that might be related to legislative activity.

An aide to Speaker Nancy Pelosi (D-Calif.) said the Supreme Court ruling “gives the executive and legislative branches the time to work out procedures that protect both the interests of law enforcement and the safeguards for Speech or Debate contained in the Constitution.”

The appeals court essentially directed the two sides to work out a deal. “There would appear to be no reason why the Congressman’s privilege under the Speech or Debate Clause cannot be asserted at the outset of a search in a matter that also protects the interests of the Executive in law enforcement,” the court wrote in its Aug. 3 ruling. “How that accommodation is to be achieved is best determined by the legislative and executive branches in the first instance.”

The Justice Department asked to the Supreme Court to overturn the appeals court ruling, arguing that the decision was already being used to challenge “searches of other places and a wide range of other investigatory techniques deemed essential to ferreting out corruption by both Members of Congress and persons who deal with them.” Until the Supreme Court overturns that ruling, DOJ argued, “investigations of corruption in the nation’s capital and elsewhere will be seriously and perhaps even fatally stymied.”

But it is unclear what impact the high court’s decision will have on corruption investigations, particularly if the FBI is able to strike a deal with the House on future searches. The government has successfully prosecuted other Members of Congress without raiding Congressional offices, and Nathan points out that even under any new procedures, the assumption is that such raids would be exceedingly rare.

Still, ethics advocates are nervous about the precedent.

“I find this fairly alarming,” said Craig Holman, campaign finance lobbyist for Public Citizen. “The Speech or Debate Clause is being used not only by Jefferson but by others — it is delaying any court action on these cases to a snail’s pace.” As Jefferson’s victory emboldens others to seek protection under the Speech or Debate Clause, Holman said, “it is going to take a very, very long time before we get to the bottom of these things.”

Meanwhile, the ruling seems to open the door for Jefferson’s lawyers to pursue a wider attack on the evidence the government has gathered in his corruption trial.

The government alleges that Jefferson accepted bribes and payment to help private businesses get contracts in Africa, including accepting cash that was to be used to bribe officials in African nations. Jefferson has denied any wrongdoing.

Jefferson has argued that material submitted to the grand jury by prosecutors may have violated the Speech or Debate Clause, and has asked the U.S. District Court in Alexandria, Va., to dismiss the bulk of the charges against him. The District Court has rejected that motion, and Jefferson’s trial has been put on hold while he appeals the ruling to the U.S. Court of Appeals for the Fourth Circuit.

But the lower court has not yet ruled on another Jefferson motion asking that all evidence taken from his office — even materials not covered by the Speech or Debate privilege — be suppressed because it is the product of an unconstitutional search. Since the Supreme Court has declined to overturn the appeals court’s assessment of the search, it would appear this motion may still have to be litigated — unless the appeals court decides to throw out the charges against him.

The Justice Department has maintained that the indictment is not based on the evidence taken from Jefferson’s office. In a statement Monday, a Justice Department spokeswoman said: “We are disappointed the Supreme Court has decided not to review this matter. The Department of Justice will continue to prosecute the case.”

Jefferson’s attorney, Robert Trout, hailed the Supreme Court’s decision not to reconsider the appeals court’s ruling on the search.

“From the very moment that we learned of the FBI’s raid on a Congressional office — the first in our nation’s history — we were convinced that the Department of Justice was out of bounds. Now, almost two years later, we are gratified that our initial judgment about this unprecedented raid has finally been confirmed,” Trout said.

“We believe that the FBI sting that targeted Congressman Jefferson and the subsequent criminal prosecution of him were similarly misguided, and we expect, when that matter is finally resolved, Congressman Jefferson will be vindicated,” Trout said.

Jonathan Turley, a law professor at The George Washington University — who criticized the Justice Department in testimony about the raid before the House Judiciary Committee in 2006 — said that while the Justice Department did not need to raid Jefferson’s office to make its case against him, the raid “succeeded in giving [Jefferson] a cause for delay, it complicated the case for the trial court [and] it changed his public image … transforming Jefferson from a villain into a victim.”