New complaints against Minnesota's U.S. Attorney B. Todd Jones have surfaced in Washington, D.C., alleging mismanagement, abuse of authority and reprisal against an assistant U.S. attorney for engaging in whistleblowing "or other protected" activity.

The charges are being investigated by the U.S. Special Counsel, an independent agency that examines whistleblower cases, according to documents obtained by the Star Tribune.

Jones, acting director of the U.S. Bureau of Alcohol, Tobacco and Firearms and Explosives (ATF), is President Obama's choice to become permanent director, but has come under fire in recent months for his work with the ATF and his leadership of the U.S. attorney's office in Minneapolis.

The assistant U.S. attorney who alleges he was unfairly disciplined is Jeff Paulsen, sources with direct knowledge of the case have told the Star Tribune.

Paulsen, a well-regarded prosecutor, was among recipients of the St. Paul Police Chief's Award in 2011 for the conviction of two men in a brutal 2007 triple homicide. He was the first assistant under former U.S. Attorney Rachel Paulose.

Paulsen has been reassigned from prosecuting high-profile criminal cases to spending a large amount of time on cases under appeal. He declined to comment on the whistleblower case.

Jones declined to comment on the allegations Wednesday. "Todd is not making any public statements pending his confirmation hearings," said Jeanne Cooney, a spokeswoman for the U.S. attorney's office.

Cooney declined to confirm that Paulsen was suspended or that he filed allegations with the Special Counsel. She said the office does not comment on personnel issues as a matter of policy.

Letter mentions allegations

The whistleblower allegations are mentioned in an April 12 letter to the U.S. Senate Judiciary Committee, which is weighing Jones' nomination. Carolyn Lerner, who heads the office of the Special Counsel, wrote the letter in response to an inquiry by Sen. Chuck Grassley, R-Iowa. Grassley is the ranking Republican on the committee and a critic of Jones' work with the ATF.

Lerner wrote that an assistant U.S. attorney, whom she does not name, alleged that a member of Jones' staff was suspended and received a "lowered performance appraisal … in retaliation for protected whistle-blowing or other protected activity."

The allegation was lodged March 12. After an initial review, the counsel decided on April 12 to conduct an investigation.

Lerner wrote that her office is also reviewing a second allegation by the same attorney, who "alleges gross mismanagement and abuses of authority in the Narcotics Violent Crime Section" of the Minneapolis office.

She said no decision had been made whether to refer the case for investigation by the U.S. Department of Justice.

Her letter mentions Grassley's inquiry about an anonymous letter critical of Jones dated July 20, 2012, and signed by "Employees of the U.S. attorney's office, District of Minnesota."

Lerner wrote that her office turned the letter over to an analyst, then closed the case on Aug. 30 because it "did not have enough information to initiate a substantive inquiry into the concerns raised by the letter."

Cooney said, "We will not comment on the anonymous letter which may or may not have been written by anyone in this office."

Nomination all but on hold

The latest disclosure deepens Jones' problems in the Senate, where GOP resistance has all but put his nomination on hold.

An aide to Judiciary Committee Chairman Patrick Leahy, D-Vt., said he is "making an assessment of the merits of the claims" so the committee can move forward.

But three months after Obama nominated Jones to the ATF post, the committee has yet to schedule a hearing on the nomination.

Both Democratic senators from Minnesota who serve on the Judiciary Committee remained noncommittal Wednesday.

A spokesman for Al Franken said he "plans to review any information that comes from the Office of Special Counsel's investigation, along with any additional information provided to the Committee about Mr. Jones."

Sen. Amy Klobuchar's spokeswoman Brigit Helgen said, "While Senator Klobuchar is not aware of all the details of the investigation, she hopes it's resolved soon and would like to see the nomination hearing move forward."

Paulsen has been with the U.S. attorney's office for 24 years. Over the past two years, he and his supervisor, Carol Kayser, have been at odds over the prosecution of narcotics and gang cases, sources said, and their working relationship deteriorated to the point where Paulsen felt he was being unfairly targeted.

The allegations being investigated by the Special Counsel were first reported Tuesday in Roll Call, a Washington, D.C., online news publication. It did not name Paulsen.

Cooney said the Minneapolis U.S. attorney's office, like others around the country, has been ordered by the U.S. attorney general to tighten internal controls and heighten scrutiny after the heavy criticism the attorney general's office received over the Operation Fast and Furious gun scandal in Arizona.

Previously, assistant U.S. attorneys had more autonomy, Cooney said. "Whenever there is change, there is some resistance," she said. "It's common."

In an interview in December, Jones had characterized complaints about his office as a reaction to his decision to shift priorities away from street-level crimes to more complex crimes involving drug cartels and to time-consuming white-collar crimes and terrorism cases.

In January, the Judiciary Committee received a letter from Donald Oswald, former director of the Minneapolis office of the FBI, who said Jones was "a significant impediment for federal law enforcement to effectively protect the citizens of Minnesota from violent gang, drug and gun activities." • 612-673-4224 612-673-1745