NPR's National Security Correspondent Mary Louise Kelly said she had spoken to a White House official on Wednesday, who succinctly described a scene of chaos. "I just reached somebody inside the White House today and asked them to describe, what's the mood like in there? What's going on in the halls?" " Kelly told the NPR Politics Podcast. "And this official said, it is an absolute effing trainwreck"
Ms Kelly also described "a lot of empty desks in the basement of the West Wing," which is where senior members of the National Security Council usually reside, after many abandoned their roles after clashing with the Trump administration.
Citing her sources, Ms Kelly said nobody was sure who was “steering the ship” anymore, and added the White House was, “to put it charitably, in upheaval”.
Mr Flynn handed in his resignation earlier in the week, amid mounting controversy over his interaction with Russian officials. Senior staff in Mr Trump’s team were told a month ago by the acting US attorney general they feared the falsehoods made him vulnerable to potential blackmail from Moscow, but the administration took weeks to act.
Ms Kelly said the National Security Council was already adjusting to major changes before the scandal erupted, destabilising it further.
When Mr Trump took office a lot of security staff who were on loan to the council chose to return to their home agencies rather than work for the new president. In addition, Mr Trump made several new appointments including the new department heads.
Mr Flynn's resignation, just weeks after he took on the role, has propelled the department into a state of chaos.
"There’s huge upheaval," Ms Kelly said. "There are literally a lot of empty desks in the basement of the West Wing, which is where the NSC is camped out."
She said it was difficult to overstate the importance of the role Mr Flynn had occupied, and questioned if the President could possibly have been prepared for his meeting on Wednesday with the Israeli Prime Minister, under the circumstances.
"Who briefed the President before this meeting today?" she said, referring to the gap left by Flynn. "Benyamin Netanyahu was walking into a White House that, to put it charitably, was in upheaval.
"The National Security Adviser's job is to bring together all the different points of view, coming from all the bureaucracies around Washington, and brief the president with this detailed thoughtful process so the US goes into a meeting knowing what they're trying to get out of it.
"Is this process happening? There’s an acting security adviser who has been there for all of 30 hours at this point..." she said.
The staff who remain in the NSC appear to be trying to get on with their jobs she said, but it was difficult without leadership.
Senator John McCain has also voiced concerns about the NSC. Speaking to NPR's Congress correspondent, he said: “You’ve got to go through a regular process of decision making and that’s what they’re not doing.
"...Who’s making the decisions in the White House? Is it the 31-year old [adviser Stephen Miller]? Is it Mr Bannon? The chairman of the joint chiefs of staff?... I don’t know."
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