Army Gen. Raymond Thomas Reuters/Kevin Lamarque

The head of the United States' clandestine military operations said on Tuesday 14 February that the "unbelievable turmoil" at the highest levels of the Trump administration is hampering the country's ability to fight threats like Islamic State (ISIS).

During a talk at a military symposium in Maryland yesterday, Army General Raymond Thomas of the United States Special Operations Command said: "Our government continues to be in unbelievable turmoil. I hope they sort it out soon because we're a nation at war."

Thomas' unit oversees special forces and secret operations like those of the Navy SEALs and Green Berets.

His comments fell on the heels of a tumultuous 24 hours in which President Donald Trump's top national security advisor Michael Flynn resigned amid scandal.

It was revealed that Flynn mislead Vice President Mike Pence and other top White House officials about conversations he had with Russia's ambassador to the US.

Details of the conversations were leaked to the press. They showed that during the transition after the election Flynn had discussed the possibility of lifting sanctions that were being imposed by President Barack Obama in retaliation for Russia's attempts to influence the US election.

Further revelations were made to The New York Times on Tuesday of how intercepted calls show members of President Trump's election campaign were repeatedly in contact with senior Russian intelligence officials in the year before the election.

The conversations were intercepted while evidence was coming to light of Russia's involvement in hacking the emails of US political figures. The Times cited four current and former American officials with knowledge of the calls.

Flynn's resignation and the revelation of the calls have prompted Democrats and some Republicans to demand a full, bi-partisan investigation.

During his talk Thomas said that when he met with Trump during his tour of MacDill Air Force Base in Tampa, Florida that the president gave "a very profound statement of support".

The two, he said, had "a very open conversation on what do you need, the strategy you need to win" against threats like Isis, adding Trump was concerned with "what do we need to get there?"

The goals Thomas discussed with Trump won't be achievable, he said, without a stable chain of military command at the top levels of the government. "As a commander, I'm concerned our government be as stable as possible," Thomas said.