If confirmed by the Senate, Mr. Johnson, 56, will fill the vacancy left by Janet Napolitano, who resigned in July to lead the University of California system.

Mr. Johnson — whose first name is pronounced “Jay” — has little experience with some of the issues that Ms. Napolitano faced, like border security and immigration. But he was a legal adviser to Mr. Obama during his first presidential campaign and has similar views to the president’s about the future of the United States’ counterterrorism operations. He was at the center of Mr. Obama’s first-term efforts to re-evaluate the counterterrorism policies of President George W. Bush.

During his tenure at the Defense Department, Mr. Johnson shaped the Obama administration’s policies on the detention of terrorism suspects and on targeted drone strikes in Yemen and Somalia. He also helped lead the drive to end the “don’t ask, don’t tell” law that had barred gay men and lesbians from serving openly in the military.

In an address at the National Defense University in May, Mr. Obama echoed Mr. Johnson in warning about the need to fight terrorism without being on a “perpetual wartime footing.”

“Our systematic effort to dismantle terrorist organizations must continue,” the president said. “But this war, like all wars, must end. That’s what history advises.  That’s what our democracy demands.”

Mr. Johnson had said close to the same thing shortly before leaving his Pentagon job in December 2012. In a speech at Oxford, he looked ahead to a day when Al Qaeda was so diminished that the United States could relax its posture and end the military’s legal authority to kill and detain terrorism suspects.

“I do believe that on the present course, there will come a tipping point — a tipping point at which so many of the leaders and operatives of Al Qaeda and its affiliates have been killed or captured and the group is no longer able to attempt or launch a strategic attack against the United States,” Mr. Johnson said at the time.

But he emphasized that he was not declaring the struggle to be over, stressing the danger of Qaeda affiliates in Yemen and in North and West Africa. He also suggested that even after the armed struggle ended, there could be a need to hold some detainees legally without trial for a period of time, as happened after World War II.

Earlier in 2012, Mr. Johnson delivered a speech at Yale Law School defending the proposition that American citizens who join Al Qaeda may be lawfully targeted for killing under certain circumstances.

But he has also criticized the Obama administration for being too secretive about matters like targeted killings using drone strikes.

“The problem is that the American public is suspicious of executive power shrouded in secrecy,” Mr. Johnson said in a speech at Fordham University this year. “In the absence of an official picture of what our government is doing, and by what authority, many in the public fill the void by imagining the worst.”

Members of Congress praised Mr. Johnson on Thursday, but they also raised concerns that so many positions remained unfilled at the Homeland Security Department.

“Even with this prospective nominee, over 40 percent of senior leadership positions at D.H.S. are either vacant or have an ‘acting’ placeholder,” said Representative Michael McCaul, Republican of Texas and the chairman of the House Homeland Security Committee. “The lack of leadership at the White House is reflected in the holes in leadership at the department, and these important positions must be filled in order to fill the holes in our homeland security.”

The president will announce the nomination at 2 p.m. on Friday, according to an administration official. News of the nomination was first reported by The Daily Beast.