The dispute comes about four months before the midterm elections. The Trump administration claims that 250,000 non-citizens are registered to vote in Pennsylvania, New Jersey, Nevada and California.
"We're not trying to change the outcome; we're trying to make sure American people can trust our voting system," Department of Homeland Security Secretary Markwayne Mullin said.
Mullin said states should work with federal officials on election security.
"Every state should partner with us to work to secure this," he said.
Mullin sent letters to officials in the states identified by the administration, including Pennsylvania Secretary of State Al Schmidt, a Republican.
Asked whether a federal claim that more than 14,576 non-citizens may be registered in Pennsylvania was accurate, Schmidt said federal officials have not shared supporting information.
"The Dept. of Homeland Security has not shared the list. It has not shared the methodology, so it's hard to speak to the credibility of it at this point, but again we take any credible allegation seriously," Schmidt said.
According to the letter, the Department of Homeland Security compared publicly available voter data against internal data on non-citizens to reach its figures.
Schmidt questioned whether that approach can reliably identify non-citizens on voter rolls.
Mullin threatens to withhold aid from states that don't comply with DHS election directives
"I've been working on the issue of non-citizens voting since 2012, so almost 15 years now," Schmidt said. "When you do these sort of evaluations or investigations, and it's based on matching data, you get a lot of false positives."
Schmidt said the federal government has not revealed the exact methodology used in its investigation and added that it is "incredibly rare" for a non-citizen to vote.
Federal officials have warned that states that do not cooperate could lose federal election funding. According to the report, election workers also could face fines or jail time if fraud is discovered.
The federal government said it will continue searching for people it considers ineligible to vote.
"We will scrub all election records looking for illegal aliens and those who are ineligible to vote, including those that somehow voted, yet they were deceased," Mullin said.
Mullin did not present evidence that any non-citizens voted. New Jersey had not responded to requests for comment.