WASHINGTON — The chief executive of the Newseum and its parent organization the Freedom Forum is resigning from the museum of journalism and the First Amendment after three years at the helm of an institution struggling to cover its costs.

On Tuesday, James Duff announced plans to return to his previous post as chief administrative officer of the U.S. Courts under an appointment by Chief Justice John Roberts. When the chief justice calls, “it’s hard to say no,” he said. Duff had led the Newseum since 2011. He will stay on as a consultant through the end of 2014 to help raise funds for programs.

For many years the Newseum was led by former journalists from Gannett Co. and USA Today. It will now return to their care, at least for now. Former USA Today editor Peter Prichard has been named the Newseum’s CEO, pending a search for a new chief executive. Jan Neuharth, daughter of Newseum founder Allen Neuharth, will be the Freedom Forum CEO.

“My motto is preserve the best and improve the rest. That’s what we’re trying to do,” Prichard said in an interview Tuesday. “No one else in the country is doing what we’re doing, which is to try to champion the five freedoms of the First Amendment and make people better educated news consumers.”

Prichard said he is optimistic for the Newseum’s future because attendance and fundraising are on the rise. The museum had more than 800,000 visitors last year, notable in a city where most government-funded museums offer free admission, he said. The Newseum charges $23 for adults and $14 for youth.

Prichard helped build the original Newseum in Arlington, Virginia, and served as president until 2009.

Future plans call for improving and updating exhibits and possibly expanding a popular gallery about the FBI. New exhibits in 2015 will focus on coverage of President Lincoln’s assassination and the Vietnam War.

For years since opening a new facility along Washington’s Pennsylvania Avenue in 2008, the nonprofit Newseum has struggled to raise enough funds to cover its costs. Last year The Associated Press reviewed the Newseum’s finances and found it was drawing heavily on the Freedom Forum endowment to cover the bulk of its costs.

Newly released financial documents show the Newseum still ran an operating deficit in 2013, but the deficit was reduced by half to $4.3 million compared with $8.3 million in 2012. Fundraising increased from about $1.3 million in 2012 to $3.3 million in 2013, though that’s still far less than other nonprofit museums.

“We’re moving in the right direction,” Prichard said. “Long term, you don’t want to have a deficit, but our endowment is sufficient to support it for a long time. We want to broaden our base of support, and we’ll be a better institution when we do that.”

In recent years, the Newseum drew less from the endowment, which has rebounded to about $400 million.

The Newseum’s executive compensation struck some nonprofit experts as overly generous for an organization falling short on fundraising. Duff was to be paid $1.4 million in his first months on the job in 2011 as deferred compensation for retirement. The funds were to compensate for his loss of a full federal pension.

With his departure, Duff will not receive the full $1.4 million, Prichard said. Instead that amount will be prorated, though the exact payout was not revealed.

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