Nakasone took the action on the day Joe Biden was inaugurated as president.
The NSA chief was ordered on Saturday by then-acting defense secretary Christopher C. Miller to install Ellis by 6 p.m. that day.
An NSA spokesman declined to comment.
Ellis, then a political appointee, was named to the post in November after a civil service competition. His selection by the Pentagon general counsel, Paul Ney, came under pressure from the White House, according to people familiar with the matter.
But as of the weekend Ellis had not taken up the job. The delay was due in part to the need for him to complete administrative and security requirements, such as passing a polygraph test. Nakasone also had concerns about Ellis’s selection and took steps to ensure it was consistent with personnel policies that apply to senior career officials in the intelligence community.
Under pressure from Miller, the agency on Sunday announced it was moving forward with the installation, and on Tuesday, Ellis assumed his post.
Nakasone has no authority over Ellis’s hiring or firing. That power lies with the Pentagon general counsel.
Ellis could not be reached for comment Wednesday. On Saturday, he informed a reporter he did not “talk to the press” before hanging up.
Miller’s order days before the Biden administration was to take over raised eyebrows and alarmed critics who said Ellis’s appointment represented the politicization of a career job at the helm of the nation’s largest spy agency.
Critics said they feared it was an effort to “burrow in” or embed a political appointee in a career civil service position as one administration gave way to another.
Ellis’s placement on administrative leave was first reported by CBS News.
Sen. Mark R. Warner (D-Va.), now chairman of the Senate Intelligence Committee, and Sen. Jack Reed (D-R.I.), who now leads the Senate Armed Services Committee, in November asked the Pentagon acting inspector general to investigate Ellis’s selection. They raised concerns of “improper political influence” and also that Ellis was picked over other more qualified candidates.
Concerns with Ellis are linked to his relationship with Rep. Devin Nunes (R-Calif.), a Trump loyalist whom Ellis helped gain access to intelligence documents in early 2017 to buttress President Donald Trump’s political attacks against Democrats. Ellis served as chief counsel to Nunes when Nunes chaired the House Intelligence Committee.
Ellis also was caught up in the controversy surrounding the prepublication review of former national security adviser John Bolton’s book for classified information. According to Ellen Knight, a former career White House official in charge of the review, Ellis tried to prevent the release of a portion of the manuscript that dealt with Ukraine and that presumably would be damaging to Trump were it to come out during his 2020 impeachment trial in the Senate.
Ellis also conducted his own review of the manuscript and, as a political appointee, countermanded the career officials’ conclusion that the book was cleared for publication, according to Knight, who documented her concerns in a September 2020 letter.
Ellis joined the White House in 2017, when he became a lawyer on the National Security Council, and in 2019, he was elevated to senior director. He held that position as recently as earlier this month.