The 33-year-old left the president-elect’s transition team on December 6 following his tweets about the Pizzagate fake news story.
His father, Michael Flynn Sr., Donald Trump’s pick to be US national security adviser, has also shared fake news.
The Pizzagate hoax led to a gunman firing shots in a restaurant on December 4.
No one was injured in the incident at Comet Ping Pong in Washington DC.
The suspect told police he had turned up to “self-investigate” online rumor-mongering that the pizzeria was the nexus of a pedophile ring involving Hillary Clinton and one of her aides, John Podesta.
The bizarre and unfounded theory had been spread online by right-wing blogs.
The claims were also pushed by Michale Flynn Jr., who tweeted after December 4 gunfire that Pizzagate would remain a story until “proven to be false”.
The New York Times reports that he was fired from the Trump transition team on December 6 but, according to CBS News, he resigned before he was sacked.
The Trump team confirmed the departure of Michael Flynn Jr. – who had reportedly been given a .gov email address – but did not confirm it was related to the tweets.
Vice President-elect Mike Pence acknowledged that Michael Flynn Jr. had been helping his father with scheduling and administrative items during the transition but said “that’s no longer the case”.
Asked repeatedly whether a security clearance was requested, Mike Pence refused to answer directly.
Michael Flynn Sr., 57, has also tweeted out unsubstantiated conspiracy theories accusing Hillary Clinton and her aides of child-s** trafficking.
Among the retired lieutenant general’s other tweets was an allegation that President Barack Obama was a “jihadi” who “laundered” money for terrorists.
Critics have said Michael Flynn Sr. is unfit to advise Donald Trump on the veracity of national security threats facing the US.
In December 4 armed confrontation, the suspect allegedly walked into Comet Ping Pong and pointed a rifle at an employee before firing shots into the ground.
Edgar Maddison Welch, 28, from North Carolina, has been charged with assault with a dangerous weapon.
The Pizzagate theory originated on alternative message board 4chan, based on emails hacked from the Democratic Party and leaked by WikiLeaks.
The restaurant’s owner, James Alefantis, a Democratic Party donor, appears in the emails in relation to organizing a Democratic fundraiser.
Users of 4chan and Reddit had said words in the emails such as cheese, hot dog, and pizza were code for young children and s** acts.
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