White House officials said Mr. Bolton came into his job determined to streamline the National Security Council, which they said had become bloated during the Obama administration, with functions that often overlapped those of the agencies. They insist his approach was welcomed: During his first breakfast with Defense Secretary Jim Mattis, one official said, Mr. Mattis asked Mr. Bolton to hold fewer meetings.

But there is a long distance between standard-issue jokes about too many meetings and eliminating them completely. Pentagon officials said Mr. Bolton did away with much of the process put in place by Mr. McMaster, a retired three-star Army general, who placed great emphasis on meetings, where everyone got a say.

Mr. Bolton’s preference, one official said, is to have one-on-one conversations with cabinet members or other senior officials directly, rather than in a group or on a conference call. He maintains more control of the process that way, this person said.

Patrick M. Shanahan, the acting defense secretary, has taken advantage of this channel, according to another Pentagon official. He has not hesitated to call Mr. Bolton directly, something that Mr. Mattis apparently did not do as much. He tended to relay questions through his recently departed chief of staff, Kevin Sweeney.

The National Security Council engaged in “reverse engineering” under Mr. McMaster as well. But officials said the trend had gotten worse under Mr. Bolton, in part because he did not trust the national-security bureaucracy and saw no reason to include it in policymaking.

Mr. Bolton is also handicapped by not having a deputy, who traditionally coordinates policy debates. He has yet to replace Mira Ricardel, an official who was forced out of the White House after she clashed with the first lady, Melania Trump.

Unlike in the past, when the National Security Council was the president’s clearing ground for security policy, one official said that the N.S.C. under Mr. Bolton was best described as another voice at a table crowded with advisers vying for influence with Mr. Trump.