A federal judge ruled Sunday that Iowa can continue to challenge the validity of hundreds of ballots from potential noncitizens despite criticism that the efforts could threaten the voting rights of recently naturalized US citizens.

In the ruling, US district judge Stephen Locher sided with the state in a lawsuit brought by the American Civil Liberties Union on behalf of an Iowa Latino group and four recent citizens who had been placed on a list of questionable registrations by local elections officials.

Iowa’s Republican attorney general and secretary of state had argued that potentially removing 2,000 names from the list would prevent illegal voting by noncitizens, a move in keeping with other Republican-led efforts across the US.

Voting by non-citizens is a Trump campaign issue, despite its rarity.

In the Iowa ruling, judge Locher pointed to a US supreme court decision last week that allowed Virginia to resume a similar purge of its voter registration rolls. Locher, a Biden appointee, also noted the appeal court’s refusal to review a Pennsylvania appeals decision on provisional ballots.

The judge noted that Iowa’s does not remove anyone from the voter rolls, but rather requires some voters to use provisional ballots.

“Today’s ruling is a victory for election integrity,” Iowa governor Kim Reynolds, a Republican, said. “In Iowa, while we encourage all citizens to vote, we will enforce the law and ensure those votes aren’t cancelled out by the illegal vote of a non-citizen.”

Rita Bettis Austen, legal director for the ACLU of Iowa, said her group was “obviously disappointed” with the decision “which we still fear threatens to disfranchise eligible voters simply because they are people who became citizens in the past several years”.

Iowa secretary of state Paul Pate and state attorney general Brenna Bird said the state had about 250 noncitizens registered to vote but the Biden administration hadn’t forwarded information on them, and the state had relied on a list of potential noncitizens from the Iowa department of transportation.

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“Today’s court victory is a guarantee for all Iowans that their votes will count and not be canceled out by illegal votes,” Bird said in a statement.

The ruling came after a federal judge stopped a similar program in Alabama challenged by civil rights groups and the department of justice. In that case, testimony showed that roughly 2,000 of the more than 3,200 voters pushed off voter rolls were actually legally registered citizens.

Locher said that it appeared to be undisputed that a number of names listed as registered voters are not in fact US citizens. But the battle over registered voters between the two main parties is unlikely to abate before or after Tuesday’s presidential vote.