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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 US 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.

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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 “preempted 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. Governor Sam Brownback of Kansas, a Republican, signed a similar law in 2011.

In an interview, the Arizona attorney general, Tom Horne, also a Republican, said, “This decision is an important victory against the Obama administration because it ensures that only US citizens, and not illegals, vote in Arizona elections.”

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The secretary of state of Kansas, Kris W. Kobach, a Republican and one of the most forceful advocates nationally against illegal immigration, called the ruling “a win for states’ rights.” He added, “We have now paved the way for all 50 states to protect their voter rolls and ensure that only US citizens can vote.”

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.

Defenders of voter identification laws argue that fraud is hard to detect but still a real danger and that Americans uncomplainingly present identification for getting on airplanes and numerous other things, so asking the same for voting, a sacred right of democracy, is only appropriate.

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

If the ruling stands, Kansas and Arizona could be forced to maintain separate ballots covering only federal races for voters who do not provide proof of citizenship, thus excluding them from state and local races. Ultimately, though, it would allow officials to “move forward with one way of becoming a registered voter in Arizona, as Proposition 200 required when passed 10 years ago,” the state’s secretary of state, Ken Bennett, a Republican, said Wednesday.

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But Jenny Rose Flanagan, director of voting and elections for Common Cause, said, “From where I sit, eligible voters, citizens, are going to be pushed out of the process yet again because of this political maneuvering.”

The case against the Election Assistance Commission stems from a decision by its acting executive director, Alice Miller, to defer action on the requests by Kansas and Arizona to include state-specific instructions to the federal voter registration form. All four commissioner positions on the panel are vacant, as Congress has yet to confirm President Obama’s nominees.

In his ruling, Melgren raised doubts over whether Miller had the authority to make that judgment, although he did not specifically address the question.

More than 10,000 Kansas voters have had their voting rights suspended for failing to provide proof of citizenship.

In Arizona, Bennett said that since the Supreme Court’s decision, about 2,000 people who registered using the federal form had failed to provide proof of citizenship.