As the FBI continues its criminal probes into Reps. Duke Cunningham (R-Calif.) and William Jefferson (D-La.), House officials have complained to the Justice Department about FBI agents contacting staffers for the two lawmakers outside of work while seeking information on their bosses.

According to sources on both sides of the aisle, officials from the Office of the General Counsel, also known as the House counsel’s office, have contacted the Justice Department in recent months to request that FBI agents coordinate any requests for information from staffers through the their office, as has been the practice in previous corruption probes.

While it is not unusual for FBI agents to contact aides while investigating a sitting lawmaker, the concerns expressed by the Counsel’s office over these inquiries demonstrate the sensitivity of separation-of-powers concerns, as agents of an executive branch agency conduct a criminal probe of a member of the legislative branch.

Stanley Brand, who served as House general counsel from 1976 to 1983, said he also dealt with similar issues during his time in Congress as federal investigators, using aggressive tactics, pressed home investigations on lawmakers.

“There are certain protocols that need to be observed when you have these inter-branch disputes,” Branch said. “You want to give the employee the right to have that counsel there. It’s a matter of comity and respect for a co-equal branch.”

A Justice Department spokesman said the department was “committed to working with the House Counsel’s office in a cooperative manner,” although he would not comment specifically on anything related to the Cunningham or Jefferson probes, citing a longstanding Justice policy of refraining from discussion of ongoing investigations.

Another Justice Department official, however, defended the FBI’s actions, calling them a necessary component of any thorough corruption investigation.

“Staffers may complain, but that’s the job of the FBI,” said the Justice official, speaking on the condition of anonymity. “If they were not contacting the staffers, the people who might be able to provide the best information, then we’d have a problem because then they’re not doing their job.”

Officials with the House Counsel’s office declined to comment for this report.

The fear for the House leadership, however, is that Congressional staffers may be unaware that any FBI interview on issues relating to their official duties should take place in the presence of a representative from the House Counsel’s office to ensure that federal agents don’t stray into areas beyond their purview.

The Speech or Debate Clause in the Constitution protects lawmakers and their aides from being questioned about their legislative acts and speeches on the House floor. But the privilege has been consistently narrowed by the Supreme Court over the years, and former Reps. James Traficant (Ohio) and Bud Shuster (R-Pa.) had mixed success in using that privilege to derail federal corruption investigations.

Several Cunningham aides, in particular, were singled out for “harassing” or “threatening” phone calls, according to a source close to the case.

The U.S. Attorney’s Office in Southern California has been particularly aggressive in its pursuit of Cunningham, who is being scrutinized about his dealings with Mitchell Wade, former owner of defense contractor MZM Inc.

Wade purchased Cunningham’s home in San Diego in November 2003 and resold it eight months later for a $700,000 loss. At the same time, MZM was winning dramatic increases in the scope of its federal contracts. Cunningham also lived for more than a year on a boat owned by Wade, and MZM’s 527 organization donated more than $50,000 to Cunningham’s political campaigns and leadership PACs, with the California Republican being the only lawmaker to receive such donations.

Federal prosecutors executed a search warrant for Cunningham’s home on July 1 even as his attorneys were negotiating with the U.S. Attorney’s office over how Cunningham could comply with a federal grand-jury subpoena. The move angered Cunningham, who called it “an appalling abuse of government power.”

In addition, a notice of potential civil forfeiture proceedings was secretly placed on Cunningham’s home by federal prosecutors. Cunningham’s lawyers have been unable to have the notice of lis pendens removed as they seek to allow Cunningham to sell his home.

Cunningham received permission from the House ethics committee to create a legal defense fund last Thursday.

Jefferson has been targeted by the FBI in an apparent sting operation, according to media reports. Federal investigators are reportedly seeking information about possible business deals by Jefferson in Ghana and Nigeria, and connections between Jefferson and a small technology company, iGate Inc., in Louisville, Ky., are being heavily scrutinized as well. The Washington Post reported that the sting operation had been ongoing for the past year and that the FBI agents found a large amount of cash in Jefferson’s freezer during a raid last month.

Jefferson recently retained defense attorney Robert Trout of the Washington, D.C., law firm Trout Cacheris, in addition to his New Orleans-based attorney, Michael Fawer. Trout is a former federal prosecutor.

Jefferson also recently set up a legal defense fund as well.