Left uncertain is what, if anything, will happen regarding Stephen K. Bannon, the president’s chief strategist, who has played a major role in shaping foreign policy. Under the original organization plan last month, Mr. Bannon was invited to attend any National Security Council meeting led by the president and was made a regular member of the so-called principals committee of cabinet secretaries.
One senior official supportive of Mr. Bannon’s position said it would not change under any reorganization. Sean Spicer, the White House press secretary, said this week that Mr. McMaster would have full authority to organize his staff, but that any change in Mr. Bannon’s status would have to be approved by the president.
Veterans of past administrations and members of Congress from both parties criticized the decision to put Mr. Bannon on the principals committee, saying that it risked injecting politics into national security. President George W. Bush’s senior adviser, Karl Rove, was generally kept out of sensitive national security meetings. Mr. Obama’s senior adviser, David Axelrod, attended some national security meetings but was not given formal status.
The White House said the concern about Mr. Bannon’s role was overblown. But Mr. Trump was surprised by the intensity of the blowback to the initial order, and complained that Mr. Flynn had not made him understand the significance of the changes or how they would be perceived, according to senior officials.
The principals committee, led by the national security adviser, is the central body that decides foreign policy issues that do not go to the president and frames the choices for those that do. The organization chart issued last month said that the director of national intelligence and the chairman of the Joint Chiefs of Staff would attend the committee’s meetings only “where issues pertaining to their responsibilities and expertise are to be discussed.”
While the decision to give Mr. Bannon a seat was a conscious one, Mr. Trump’s team did not intend to reduce the role of the intelligence director or Joint Chiefs chairman, officials said. In crafting their organization order, the officials said, Mr. Trump’s aides essentially cut and pasted language from Mr. Bush’s organization chart, substituting the national intelligence director for the C.I.A. director, who back then was the head of the nation’s spy agencies.
What Mr. Trump’s team did not realize, officials said, was that Mr. Obama’s organization chart made those two positions full members of the committee.
As a practical matter, Mr. Trump’s aides may not have intended a substantive change, but the political symbolism of elevating Mr. Bannon while seemingly demoting military and intelligence leaders was an immediate distraction.
Even before Mr. McMaster’s appointment, White House officials were talking about revising the organization chart. The issue came to a head after Mr. Trump asked for Mr. Flynn’s resignation last week because Mr. Flynn had misled Vice President Mike Pence and other White House officials about what he discussed with Russia’s ambassador in a December phone call.
Under Mr. Flynn, the National Security Council staff, composed largely of career professionals, was unsettled by the new administration. Staff members privately complained that they were shut out of meetings on their areas of responsibility and were not fully informed about the president’s policies or communications with foreign leaders. Some said they feared that their telephone calls or emails were being monitored. For its part, Mr. Trump’s team suspected the staff members of leaking information to sabotage the new president’s plans.
While Mr. McMaster has little experience in Washington, his appointment has been welcomed on both sides of the political aisle as a sign of a more pragmatic and less ideological national security team.
Since arriving this week, Mr. McMaster has made a point of going door to door through the Eisenhower Executive Office Building, where most national security aides work, to introduce himself and build relations, current and former officials said. He is planning an all-hands staff meeting on Thursday.