Updated: 12:27 p.m.

The Senate confirmed Gene Dodaro on Wednesday night to be comptroller general of the Government Accountability Office, nearly three years after he took over Congress’ investigative arm as its interim leader.

He and other executive branch nominees were confirmed via a unanimous consent agreement reached among Senate Majority Leader Harry Reid (D-Nev.), Minority Leader Mitch McConnell (R-Ky.) and the White House in the waning hours of the 111th Congress.

They included Jacqueline Berrien, who will take her place on the Equal Employment Opportunity Commission; Jonathan Woodson, who will become an assistant secretary of defense; and Carol Fulp, who will become a general representative to the general assembly of the United Nations.

The Senate also approved a few judicial nominees before adjourning sine die Wednesday.

Dodaro was the agency’s chief operating officer for nine years. He stepped in as acting comptroller general after David Walker resigned in February 2008 to join the Peter G. Peterson Foundation, which is dedicated to raising awareness about the national debt and fiscal responsibility.

The nomination process dragged on well into 2010, with Democrats and Republicans clashing about who should be given the nod. President Barack Obama nominated Dodaro in September to a full 15-year term.

Senate Homeland Security and Governmental Affairs Chairman Joe Lieberman (I-Conn.) said in a statement that Dodaro has proved himself through his 40 years of government service.

“He has worked tirelessly to improve the performance and capacity of our government and his non-partisan leadership at the GAO has deeply informed and improved our work,” Lieberman said. “Mr. Dodaro will have no learning curve and I look forward to working with him.”

Sen. Susan Collins (R-Maine), the committee’s ranking member, also endorsed Dodaro and urged him to look for ways to make government more effective and accountable.

“Our nation desperately needs aggressive and independent oversight of the federal government,” Collins said in a statement. “We live in an era of historic deficits, crippling unemployment and smaller budgets. As the government tightens its belt, the GAO, which has been labeled ‘the American taxpayers’ best friend,’ must remain an unabashed advocate for the public and a protective steward of federal resources.”

Despite the package of executive branch nominees that managed to win confirmation in the hours before the Senate adjourned, 19 judicial nominees that had been reported out of the Judiciary Committee did not advance. They were returned to Obama.

Although the Senate confirmed five judicial nominees on Wednesday, Judiciary Chairman Patrick Leahy (D-Vt.) complained that the Republicans throughout the 111th Congress unfairly blocked qualified Obama picks to serve on the federal courts.

“These are all superbly qualified nominees, most were reported with bipartisan support and many unanimously. Thirteen of these nominations on which we are not being allowed to vote are to fill judicial emergency vacancies, as determined by the nonpartisan Administrative Office of the U.S. Courts,” Leahy said Thursday in a statement. “Yet, for month after month, many of these nominations have been stalled.”

Republicans have repeatedly argued that they have treated Obama’s judicial nominees the same way Democrats treated President George W. Bush’s selections. Additionally, Republicans have said, Obama was as willing a participant in blocking Bush’s nominees as any Democrat during his short Senate tenure.