Peter Navarro is the second Trump aide to be arrested after defying a legal summons from the congressional committee investigating the attack.
In court, Mr Navarro, 72, accused prosecutors and the FBI of misconduct.
His indictment comes a week before the committee is due to begin televised hearings on its inquiry.
The US House of Representatives panel, made up of seven Democrats and two Republicans, has interviewed more than 1,000 witnesses.
Steve Bannon, who was chief strategist to former President Donald Trump, faced contempt of Congress charges last November after he too defied a subpoena.
Mr Navarro has been charged with refusing to provide testimony or documents to the committee investigating the riot at the US Capitol on 6 January 2021.
A China hawk who advised Mr Trump on trade issues and also served on the Covid task force, he did not enter a plea at his hearing on Friday in Washington DC.
Mr Navarro faces the possibility of up to two years in jail or a fine.
He condemned the manner of his arrest earlier in the day by FBI agents at a Washington airport as he was boarding a flight to Nashville, Tennessee.
“Who are these people? This is not America,” the former economics professor said in court, according to the Associated Press news agency. “I was a distinguished public servant for four years!”
Outside, Mr Navarro protested that he had been placed in handcuffs and leg irons as he was taken into custody, reports Fox News.
He said he would represent himself, because he was not willing to spend several hundred thousand dollars on legal counsel.
The former aide has already acknowledged in media interviews that he helped co-ordinate an effort – known as the “Green Bay Sweep” – to keep Mr Trump, a Republican, in power after he lost the November 2020 election to his Democratic challenger Joe Biden.
The House panel has also recommended contempt charges for Dan Scavino, a former deputy chief of staff to Mr Trump, and Mark Meadows, who was White House chief of staff.
But it emerged on Friday evening that the US Department of Justice will not act on those two referrals.
Mr Trump has urged his former associates not to co-operate with the Democratic-led investigation, deeming it politically motivated.
Mr Navarro has claimed his communications with the former president were protected under the legal principle of executive privilege.
Critics of the investigation have pointed out that in 2012, former US Attorney General Eric Holder was not criminally charged after he was found in contempt of Congress for refusing to co-operate with an inquiry.
Then-President Barack Obama, a Democrat, had asserted executive privilege in that case.