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PHOENIX — A federal judge in Kansas on Wednesday ordered federal election authorities to help Kansas and Arizona require their voters to show proof of citizenship in state and local elections, in effect sanctioning a two-tier voter registration system that could set a trend for other Republican-dominated states.

Judge Eric F. Melgren of the U.S. District Court in Wichita, Kan., ruled that the federal Election Assistance Commission had no legal authority to deny requests from Kansas and Arizona to add state-specific instructions to a national voter registration form. The states sued the agency to force the action after it had turned them down.

The Supreme Court ruled in June that Congress holds full power over federal election rules but indicated that states could require proof of citizenship in state and local elections. Federal rules require prospective voters only to sign a form attesting to their citizenship, a procedure that is favored by Democrats. who want to increase participation of minorities and the poor in elections, but that Republican officials say fosters voter fraud.

In his ruling, Melgren, who was appointed to the bench by President George W. Bush, characterized the decision by the election commission to deny the states’ requests as “unlawful and in excess of its statutory authority.” He said that Congress had not “pre-empted state laws requiring proof of citizenship through the National Voter Registration Act.”

Proof of citizenship became a requirement in Arizona under Proposition 200, approved in 2004 — the law struck down by the Supreme Court in June — as part of the long legal and political fight against illegal immigration in this border state. Gov. Sam Brownback of Kansas, a Republican, signed a similar law in 2011.

There has been little evidence of in-person voter fraud or efforts by noncitizens to vote, but the poor and minorities are likely to be affected. Studies have shown that the poor and minorities often lack passports and access to birth certificates needed to register under the laws in question.

Melgren’s decision holds particular significance this election year, as it could prevent thousands of people from voting just as the governorship and other major offices are on the ballot in both states.

The ruling takes effect immediately unless the courts grant a stay pending an appeal. The Justice Department said that it was reviewing the court’s decision.