Story highlights It wasn't exactly clear what Thomas was referring to

But his remarks come soon after Michael Flynn was forced to step down as national security adviser

Washington (CNN) The head of US Special Operations Command said Tuesday that the US government is in "unbelievable turmoil," a situation that he suggested could undermine US efforts to fight adversaries such as ISIS.

"Our government continues to be in unbelievable turmoil. I hope they sort it out soon because we're a nation at war," Army Gen. Raymond "Tony" Thomas told a symposium in Maryland.

While it wasn't exactly clear what Thomas was referring to, his remarks come less than 24 hours after retired Lt. Gen. Michael Flynn was forced to step down as national security adviser, becoming by far the shortest tenured adviser in history.

Thomas oversees America's elite Special Operations troops, including Navy SEALs and Army Green Berets, which have played a large role in carrying out the nation's conflicts since 9/11.

Asked later about his comments, Thomas, a veteran of Iraq and Afghanistan, said: "As a commander, I'm concerned our government be as stable as possible."

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