PHOENIX — A federal judge on Wednesday ordered the Election Assistance Commission to require would-be Arizona voters to provide proof of citizenship when they register.

Judge Eric Melgren ruled that Alice Miller, the federal commission’s acting director, acted illegally in refusing to amend voter registration forms to comply with Proposition 200, a 2004 voter-approved Arizona law linking citizenship proof to voting. Melgren said Miller cannot substitute her own judgment of what is necessary to prove citizenship to what state elected leaders and voters have decided.

Wednesday’s ruling is a setback for the Mexican American Legal Defense and Educational Fund, which argued on behalf of several groups that the Arizona requirement undermines their voter-registration drives. Unless overturned, it could complicate the ability to register new voters who may not be carrying or have access to the  proof Arizona requires.

MALDEF attorney Nina Perales promised an appeal.

“The U.S. Supreme Court has already spoken on this issue and ruled that state laws like Prop. 200 must yield to federal law,” she said.

Attorney General Tom Horne called it a key victory in preventing voter registration fraud.

“This order compels action immediately,” he said of Melgren’s direction to the commission. “So we’re going to make sure that only citizens vote in the 2014 election.”

Horne said there is no conflict between Wednesday’s ruling and prior Supreme Court rulings. He also said that there  is a vote-fraud problem in Arizona.

“There’s been a cover-up by the media of the extent to which voter fraud is a problem in Arizona,” Horne said. He said some reporters — he would not say whom — have ignored the original findings of U.S. District Judge Roslyn Silver, which he said “concluded voter fraud is a significant problem in Arizona.”

Silver’s 2009 ruling upholding the proof-of-citizenship requirement, however, says only that the state “demonstrated instances of voter fraud in Arizona.” She said  that Proposition 200, the 2004 measure, “enhances the accuracy of Arizona’s voter rolls and ensures that the rights of lawful voters are not debased by unlawfully cast ballots.”

That 2004 measure requires both proof of citizenship to register and identification when casting a ballot.

Legal efforts to kill the latter requirement faltered early in the process and the ID provision remains on the books.

Arizona has been entitled since the 2004 vote to require documented proof of citizenship for those who use  the state-designed form to register.

This fight surrounds the fact that Congress empowered the Election Assistance Commission to design a national voter-registration form. That form requires no proof of citizenship — only that those registering swear, under penalty of perjury, that they are eligible to vote.

Last year the U.S. Supreme Court rejected Arizona’s attempt to enforce the proof-of-citizenship requirement on those using the federal form. That is the ruling on which Perales is counting.

The justices, however, said the state remains free to petition the commission to change its form.

But Miller, acting alone because all commission posts are vacant, refused. That led to this lawsuit by both Arizona and Kansas, which adopted a similar law last year.

Miller, in her January order, said Arizona showed no need for additional documents.

“Arizona’s evidence at most suggests that 196 of 2,706,223 registered voters, approximately 0.007 percent, were unlawfully registered noncitizens around the time that Proposition 200 took effect,” she wrote at the time.

Miller said allowing Arizona to require proof of citizenship at time of registration “would thwart organized voter registration programs” because people do not always carry  documents that Arizona considers acceptable proof of citizenship.

That runs afoul of what Congress wanted in mandating a federal form to “facilitate voter registration drives,” she said.

Melgren, in Wednesday’s 28-page ruling from Wichita, Kan., said that is legally irrelevant.

“The Arizona and Kansas legislatures have decided that a mere oath is not sufficient to effectuate their citizenship requirements and that concrete proof of citizenship is required to register to vote,” he wrote. And he said the U.S. Constitution gives states “exclusive authority” to set voter qualifications.

What that means, Melgren wrote, is that the commission must bow to each state’s determination “that a mere oath” is insufficient to determine someone is qualified to vote.

How that ruling might affect Arizona voter registration if not overturned is unclear.

Arizona law allows a driver’s license issued after 1996 to be used as proof.

Perales, in her legal briefs, cited testimony from Debra Lopez, who has been involved with the Latino Vote Project.

According to Perales, Lopez said those who do not have a license will be required to produce something else proving citizenship. And that, Perales said, would require Lopez to bring a copy machine to registration events.