WASHINGTON -- For three years, Rep. Alan Mollohan has chaired the important Appropriations subcommittee that controls the Justice Department's $65 billion budget. At the same time, he has been under Justice Department investigation, according to documents and two sources briefed on the probe.

The inquiry has centered on the West Virginia Democrat's finances and nonprofits he created and helped fund in his district, and has put him in the unusual position of wielding control over an agency as it is probing his conduct and contractors he helped while in office.

Some congressional watchdog groups, including the one whose complaints about Mr. Mollohan triggered the probe, think the House leadership has created a clear conflict of interest by allowing him to continue to chair the subcommittee.

"There are a hundred ways he can influence what happens with the department's funding -- without one vote. Everything goes through his committee," said Ken Boehm, chairman of the National Legal and Policy Center, a conservative watchdog group that alleged in a complaint that the congressman had not reported the nature and increasing value of his real estate investments. "If that's not a conflict of interest, I don't know what is."

Mollohan spokesman David Herring said the congressman dealt with the issue in 2006 by recusing himself from voting on specific budget accounts for the FBI, the attorney general's office and other investigative functions. Mr. Herring declined to release the letter describing that recusal to House leaders. The spokesman also said Mr. Mollohan is not aware of the Justice Department inquiry and has not been contacted by investigators.

Ethics inquiries into Mr. Mollohan date to 2006, when Mr. Boehm filed a complaint with the Justice Department. The complaint focused attention on Mr. Mollohan's assets, which had jumped in value from $562,000 in 2000 to at least $6.3 million in 2004. At the same time, he had steered $250 million in earmarks to nonprofit groups whose leaders were sometimes investors with him.

Mr. Mollohan initially cast Mr. Boehm's complaint as a Republican-funded smear campaign, but in June 2006, he corrected several previous financial disclosure forms and reported that he had received a loan from a director of one of the nonprofits. He also hired a legal defense team, and spent more than $157,000 in legal fees in the 2008 election cycle.

In the spring of 2006, news broke that a federal grand jury in West Virginia was examining him. Back on Capitol Hill, then-Democratic leader Nancy Pelosi of California urged Mr. Mollohan to give up his seat on the House ethics committee, which he did.

After becoming House speaker in January 2007, Ms. Pelosi defended her decision to let Mr. Mollohan remain as a powerful "cardinal" over the Appropriations subcommittee. "Quite frankly, I think the Justice Department is looking into every member of Congress. I always say to everybody, 'You're now going to get a free review of your family tree -- past, present and future, imagined and otherwise,' " she said then.

A Pelosi spokeswoman said she thinks Mr. Mollohan's recusal from specific votes addresses potential conflicts.

After a flurry of subpoenas for nonprofit records in 2006 and 2007, the Justice Department probe went quiet. News that it was still under way was detailed in a document created by House ethics investigators obtained last month by The Washington Post after a computer security breach.

The document listed the status of ethics inquiries into more than two dozen members of Congress.

Washington correspondent Daniel Malloy writes the "Pittsburgh On The Potomac" blog exclusively at PG+, a members-only web site of the Pittsburgh Post-Gazette. Our introduction to PG+ gives you all the details.