Flynn's replacement, Lt. Gen. H.R. McMaster, has freely made changes to the national security structure since assuming the role. McMaster immediately expressed a desire to run a less hierarchical organization and be more accessible to his staff.
Another White House official, Dina Powell, was recently named deputy national security adviser for strategy and has been present in the recent high level meetings with delegations from Saudi Arabia, Egypt, Jordan and China. Powell joined the White House to work with Trump daughter Ivanka on women's empowerment issues. She had previously served as assistant secretary of state for educational and cultural affairs under President George W. Bush before joining Goldman Sachs.
But Powell soon began attending senior-level staff meetings with the president himself. Her promotion to deputy national security adviser last month triggered early speculation that McFarland's days on the National Security Council were numbered.
On Thursday, as the president huddled with top national security and Cabinet officials to trigger U.S. missile strikes on Syrian government installations from a newly built situation room at Trump's Florida resort, Powell was among the attendees. McFarland was not.
McFarland had been working as a Fox News analyst before joining Trump's national security team. She previously worked for three Republican presidents — Richard Nixon, Gerald Ford and Ronald Reagan.
Among the most notable changes to take place under McMaster was the removal of Trump's chief strategist, Steve Bannon, from the National Security Council, reversing an earlier, contentious decision to give Bannon access to the group's highest-level meetings.
A senior White House official said Wednesday that Bannon was initially placed on the National Security Council during Flynn's tenure as a measure to ensure implementation of the president's vision, including efforts to downsize and streamline operations at the NSC, and that McMaster quickly gained the confidence of the administration, eliminating the need for additional oversight.
A new memorandum about the council's composition, published Wednesday in the Federal Register, also reflected that the director of national intelligence and the chairman of the Joint Chiefs of Staff, as well as the energy secretary, had been restored as members of the principals committee.
The changes come as Trump's White House faces allegations that it funneled secret intelligence reports to a Republican congressman leading an investigation into his campaign's possible ties to Russian officials as well as Moscow's interference in the 2016 election. The New York Times last month identified two NSC officials as having helped House intelligence committee Chairman Devin Nunes view secret reports that showed Trump and his associates were incidentally swept up in foreign surveillance by U.S. intelligence agencies.
The senior White House official said the changes were not in response to the recent controversy linked to the NSC.