A senior official in his department resigned after US Attorney General William Barr told federal prosecutors to look into any "substantial" allegations of voting irregularities.
The justice department official who would have overseen such investigations, Richard Pilger, quit in response to Mr Barr's memo, BBC reported.
"Having familiarised myself with the new policy and its ramifications... I must regretfully resign from my role," he wrote in an email to colleagues.
The attorney general wrote that inquiries could be made by federal prosecutors "if there are clear and apparently-credible allegations of irregularities that, if true, could potentially impact the outcome of a federal election in an individual State".
Mr Barr said prosecutors should only look into "substantial allegations" of irregularities, and that "specious, speculative, fanciful or far-fetched claims" should be ignored.
He acknowledged that individual states had the primary responsibility for the conduct of elections, but said the justice department had "an obligation to ensure that federal elections are conducted in such a way that the American people can have full confidence in their electoral process and their government".
Democrat Joe Biden's projected win on Saturday took him over the threshold of 270 electoral college votes needed to secure victory nationwide.
President Donald Trump refuses to admit losing the vote, making unsubstantiated claims about voter fraud.
His spokeswoman vowed the legal battle to contest Mr Biden's victory was only just beginning.
"This election is not over," White House press secretary Kayleigh McEnany told a news conference. "Far from it."
Separately the Trump campaign filed a lawsuit on Monday in a Pennsylvania federal court, seeking an emergency injunction to stop state officials from certifying Mr Biden's victory in the state. The state's Attorney General Josh Shapiro called the lawsuit "meritless".
Prosecutors in Republican-controlled states meanwhile threw their weight behind the president's challenge to the election results.
The 10 state attorneys general filed a so-called amicus brief at the US Supreme Court backing the Trump campaign's case in Pennsylvania.