The Justice Department’s top leadership, some of which had been in flux because of partisan battles over nominees, has stabilized with the Senate’s confirmation of three high-level officials.

The Senate last week gave final approval to James M. Cole as deputy attorney general, Lisa Monaco as assistant attorney general for national security and Virginia Seitz as assistant attorney general of the Office of Legal Counsel. Cole’s confirmation ended a year-long battle with congressional Republicans, while Seitz’s position was at the center of a standoff lasting more than two years.

All three are vital jobs, Justice Department officials say. The deputy attorney general runs the sprawling department as essentially a chief operating officer, while the department’s national security division melds counterintelligence and law enforcement in an effort to prevent terrorist attacks. The Office of Legal Counsel provides legal advice that has traditionally carried great weight within the executive branch.

Although the delays did not impair critical functions and Cole had been serving as deputy since January under a recess appointment by President Obama, officials had long emphasized the need for a Senate-confirmed deputy.

“In Washington, the confirmed nominee is perceived to have more capital,’’ said Paul J. McNulty, deputy attorney general in the George W. Bush administration. “And Washington is a place where the amount of capital makes a very significant difference in the ability to get things done and to be heard.’’

All three confirmations, McNulty said, will give Attorney General Eric H. Holder Jr. “the leadership he has to depend on in order to run the department.’’

Holder said in a statement that he was pleased with all three confirmed nominees. “I’m confident they will provide invaluable leadership to the department,’’ he said.

Cole, a former 13-year Justice Department official and white-collar defense lawyer who is a longtime Holder friend, had been among the Obama administration’s most embattled nominees.

Nominated in May 2010, he was blocked by Senate Republicans, who criticized comments he had made about the fight against terrorism and his tenure as an independent monitor at AIG before the 2008 financial collapse.

After the recess appointment, which allowed Cole to serve through December, the administration made a renewed push for his nomination.

Sen. Charles E. Grassley (Iowa), the ranking Republican on the Senate Judiciary Committee, urged Republicans to block a vote because he was dissatisfied with the Justice Department’s handling of his request for documents related to the Bureau of Alcohol, Tobacco, Firearms and Explosives’s “Fast and Furious” anti-gun-trafficking operation. After Grassley reached an agreement with the department and other senators, Cole was confirmed 55 to 42, with three senators not voting. Grassley voted no, saying he had “serious concerns” about Cole’s qualifications.

Seitz, a former appellate lawyer at Sidley Austin’s Washington office, was confirmed in a unanimous voice vote. She becomes the first confirmed head since 2004 of the office made famous during the Bush administration as the place where controversial memos on executive power, the waterboarding of terrorism suspects and warrantless eavesdropping won support.

Seitz’s ascension was a quiet end to a struggle that began in March 2009, when Obama nominated law professor Dawn E. Johnsen for the post. Some Republicans objected to her criticism of the Bush administration’s interrogation policies, while others expressed concern over her legal work for an abortion rights group.

With her nomination languishing, Johnsen withdrew in April 2010, citing “lengthy delays and political opposition.”

Seitz, who was nominated in January, said in her Senate confirmation hearing in March that the office “ is primarily a reactive office. . . . We don’t really set an agenda. The country sets the agenda for that office.’’

If confirmed, she said, she would do her best “to give the candid, principled and independent advice that that office is called on to give.’’

Johnsen, a law professor at Indiana University, called Seitz “a terrific lawyer” and said her confirmation was important. “We’ve seen at different times in our history that ensuring that the president acts lawfully can be a tough job,’’ Johnsen said. “It’s a grave mistake to make that more difficult by not having someone with the full authority of the office.’’

Legal observers have pointed to the White House debate over the military operation in Libya as an example of the need for a strong Office of Legal Counsel. Advisers from the office, along with the Pentagon, told Obama they believed the U.S. actions in the Libya campaign should be considered “hostilities,” sources have said.

Obama accepted the opposing views of White House counsel and the State Department, the sources said. That allowed him to bypass the 1973 War Powers Resolution, which requires that U.S. forces be withdrawn from hostilities within a certain period unless Congress approves continued military action.

Monaco, also unanimously confirmed, had been the Justice Department’s principal associate deputy attorney general and is a former chief of staff to FBI Director Robert S. Mueller III.

In her May confirmation hearing, Monaco said she would “give my all” to protect the nation from attacks. She also vowed to continue the department’s crackdown on leaks of sensitive information. The Obama administration has brought more leak-related prosecutions than any administration before it.

The cases “reflect a stepped-up effort and indeed a priority placed on the prosecution of leak matters in the department,’’ Monaco said. “Leaks are — they do tremendous damage. . . . These are very, very important prosecutions.’’

Staff reporter Felicia Sonmez contributed to this report.