Two of the roughly 36 sites seized included Iranian state-controlled news outlets, Press TV and Al-Alam.
The sites were inaccessible Tuesday afternoon and instead displayed a single page that said each site had "been seized by the United States Government."
The Iran-backed Houthi rebel satellite news channel, Al-Masirah in Yemen, was also targeted by the Department of Justice (DOJ).
The group said the shutdown came without warning, but it promised to continue its mission of "confronting the American and Israeli acts of piracy against our nation, by any means."
The DOJ has yet to comment on the site seizures and it is unclear what "misinformation" was propagated.
The move by the DOJ comes as tensions between the U.S. and Iran have heightened following Tehran’s presidential election Saturday.
The Biden administration's plan to bring Iran back under a nuclear arms agreement could prove more difficult with the election of judiciary chief Ebrahim Raisi.
In his first address Monday, Raisi said he had no intention of speaking with President Biden and rejected further talks of a nuclear deal.
Biden made reentering an Iranian nuclear deal a key component of his campaign after Donald Trump pulled the U.S. out of the Joint Comprehensive Plan of Action (JCPOA) in 2018, effectively rendering the agreement between the United Nations and EU ineffective.
But despite Raisi’s opposition to a nuclear deal, the Biden administration remains confident nuclear talks will continue, noting that Iran’s Supreme Leader Ayatollah Ali Khamenei – who signed the deal in 2015 – will have the final say.
"The president’s view and our view is that the decision leader is the supreme leader," White House press secretary Jen Psaki said Monday. "That was the case before the election, it’s the case today, it will be the case probably moving forward."
The White House could not be immediately reached for comment on how the Tuesday seizures may affect Iran-U.S. relations.
The DOJ is expected to release a statement detailing the media outlet closures. Check back on this developing story.
Lucas Tomlinson, David Spunt and the Associated Press contributed to this story.