An independent government watchdog is probing allegations that President Barack Obama’s nominee to lead the Bureau of Alcohol, Tobacco, Firearms and Explosives, B. Todd Jones, improperly retaliated against a whistle-blower while working in his current job as a federal prosecutor in Minnesota.

The investigation by the Office of Special Counsel is the latest complication surrounding Jones’ nomination to lead the ATF, a 5,000-employee law enforcement agency tasked with regulating the nation’s firearms industry. Obama nominated Jones on Jan. 16 as part of his broader plan to address gun violence following the mass shooting at Sandy Hook Elementary School in Connecticut.

Carolyn N. Lerner, the head of the Office of Special Counsel, wrote in an April 12 letter to Senate Judiciary Chairman Patrick J. Leahy, D-Vt., and ranking Republican Charles E. Grassley of Iowa that her office has launched an investigation into allegations that Jones retaliated against a subordinate while working as the U.S. attorney in Minnesota, a position he has held since August 2009. Jones has worked simultaneously as the ATF’s acting director since August 2011.

The subordinate, an assistant U.S. attorney, “alleges that personnel actions, including a suspension and a lower performance appraisal, were taken in retaliation for protected whistle-blowing or other protected activity,” according to Lerner’s letter, which was provided to CQ Roll Call by an aide to Grassley, the top Republican on the Senate Judiciary Committee. The assistant U.S. attorney’s complaint was filed March 11, two months after Obama nominated Jones to the ATF position.

Lerner wrote that her office is also reviewing a second complaint against Jones made by the same assistant U.S. attorney, alleging “gross mismanagement and abuses of authority in the Narcotics and Violent Crime Section of the U.S. Attorney’s Office, District of Minnesota.” That complaint, also filed March 11, is still being vetted and has not been referred for an investigation, she wrote.

Lerner added that the Office of Special Counsel has dismissed a third complaint about Jones — made in the form of an anonymous letter from “Employees of the U.S. Attorney’s Office, District of Minnesota” — “because OSC did not have enough information to initiate a substantive inquiry into the concerns raised by the letter.” The anonymous letter, which was dated July 20, 2012, and also provided to CQ Roll Call, alleged that Jones “has instituted a climate of fear” at the federal prosecutor’s office in Minnesota.

Grassley inquired about the anonymous letter in a letter to Lerner on April 8, prompting Lerner to respond and disclose the other complaints and the ongoing investigation into Jones.

The White House did not return requests for comment.

Mounting Problems for Nominee

While the Office of Special Counsel has not made any determinations about the allegations made against Jones, the inquiries are the latest indication that his nomination for a sensitive, politically charged position might be in trouble.

The ATF has lacked a permanent director since 2006, when Rep. Jim Sensenbrenner, R-Wis., inserted language into the reauthorization of an anti-terrorism law to require Senate confirmation for the position. Gun rights advocates, who have long viewed the ATF with suspicion, have opposed nominees from both parties.

Grassley has emerged as a leading skeptic of Jones and has raised a host of concerns about him, including his managerial style and his role in “Operation Fast and Furious,” a botched ATF investigation that allowed thousands of guns to enter Mexico illegally. Two of those guns were later found at the murder scene of a U.S. Border Patrol agent in Arizona.

Grassley also has pressed for answers on Jones’ involvement in an alleged agreement between the Justice Department and the city of St. Paul, Minn., in which the city withdrew from a Supreme Court civil rights case in exchange for the federal government’s offer not to join a pair of housing-related lawsuits against the city. Grassley has called the agreement a “shady deal” that may have cost the Treasury $180 million.

The Obama administration sought to address GOP concerns about the St. Paul incident by making Jones available to the Senate Judiciary Committee and other congressional staffers for a private interview about the agreement. But while that interview has helped clear up Grassley’s concerns about that aspect of Jones’ record, it did not touch on any of the other GOP concerns about the nominee, and the committee still has not scheduled a confirmation hearing for him.

Timing, meanwhile, is increasingly becoming a concern for gun control advocates, who would like to see Jones confirmed as soon as possible.

The Judiciary Committee, which spent much of February and March reviewing the president’s gun agenda, is now immersed in an 844-page immigration bill that is likely to dominate the agenda for at least the next several weeks.

Jones’ confirmation also appears to have receded as a priority for the White House.

Obama has not publicly pushed for Jones’ confirmation since Feb. 4, according to a review of his speeches on gun violence, even as he has repeatedly prodded lawmakers to take up the other aspects of his agenda, including a ban on assault weapons and high-capacity magazines and a tightening of the background check system. Those proposals were defeated on the Senate floor last week, though Obama and Senate leaders have vowed to keep pressing for them.

“At this point, I don’t know where the president goes with this,” said Harry L. Wilson, a political science professor at Roanoke College in Virginia and the author of a book about the politics of gun control. “I think this policy window, contrary to what people are saying about pressing forward, is closed.”

An earlier version of this story incorrectly stated that the Office of Special Counsel is part of the Justice Department. It is an independent investigative agency.