The Department said it filed the lawsuit based on a federal law that prohibits purges from rolls within the 90-day period leading up to an election.
"As the National Voter Registration Act mandates, officials across the country should take heed of the law's crystal clear and unequivocal restrictions on systematic list maintenance efforts that fall within 90 days of an election," said Assistant Attorney General Kristen Clarke of the Justice Department's Civil Rights Division.
The system, implemented via executive order by Gov. Glenn Youngkin, has already faced lawsuits from several immigration rights groups.
The DOJ recently filed a similar lawsuit against the state of Alabama over similar voter roll purges.
The Justice Department seeks injunctive relief that "would restore the ability of impacted eligible voters to vote unimpeded on Election Day," the department said in a statement.
In a statement on the governor's website, Youngkin called the lawsuit a "politically motivated action," and vowed to not "stand idly by."