The removals come as McMaster seeks to consolidate his control of security policy and remove loyalists to Flynn, Trump's first national security adviser who left after less than a month because of revelations that he had obscured Russian Federation ties.
"There is a split in the White House between the Bannon camp of ideologues and the McMaster-Mattis-Tillerson camp of more centrist intellectuals", Pete Mansoor, a retired Army colonel who worked closely with McMaster, told Politico.
James Carafano, a former Trump transition team official and vice president of the conservative Heritage Foundation, decried as counterproductive the recent spate of "blood-in-the-water" rumors.
McMaster, for example, dismissed top Middle East adviser Derek Harvey, last week amid reports that Harvey'd become too close to Trump's chief strategist, Stephen Bannon - a bitter rival of McMaster. McMaster accompanied Trump to Israel last May, during which he had a three-hour conversation with Defense Minister Avigdor Lieberman in Jerusalem. But McMaster has faced accusations he is anti-Israel due to his support of the Iran nuclear deal and reports that he refers to Israel as "the occupying power". During a July 19 meeting in the White House Situation Room, Trump demanded that his top national security aides provide more information on what one official called "the end-state" in a country where the United States has spent 16 years fighting against the Taliban with no end in sight. Both men, for instance, agreed that the Trump administration should certify that Tehran is complying with the Iran nuclear deal - a pivotal decision that Trump resisted last month despite concerns that not issuing the certification would infuriate United States allies and forfeit all current restrictions on Iran's nuclear program.
General McMaster had sought to remove him in March when Central Intelligence Agency leaders raised concerns about him, but Mr Cohen-Watnick appealed to Mr Trump's top advisers, Steve Bannon and Jared Kushner.
For the time being though, McMaster's position seems safe, with a senior White House official telling the New York Times Friday that the president has "total confidence" in his national security adviser.
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Cohen-Watnick's removal comes after the revelation by The Atlantic on Wednesday of the dismissal of Rich Higgins, another Iran hawk who was the NSC's director of strategic planning. "They're taking out people who were chosen to best implement the president's policy that he articulated during the campaign".
McMaster's various moves have been noticed by Trump's base, with #FireMcMaster becoming a trending hashtag on Twitter, and a regular topic on conservative news sites - including Breitbart News.
Most members of the Council served President Obama.
Even as the White House appeared overcome by the resignations of two communications directors and a chief of staff in rapid succession, McMaster has carried out his months-long quest to clear Flynn's baggage.
Some say McMaster's "purge" is part of a larger conflict in the White House between those committed to "draining the swamp,"' and "bureaucratic interests" trying to maintain establishment control over policy.