Jackie L. Jeter, president of Amalgamated Transit Union Local 689, representing most front-line Metro workers, listens to testimony during a hearing on Feb. 25, 2010, into a fatal Metro train collision. (Bill O’Leary/The Washington Post)

A federal judge has ordered Metro’s largest union to conduct new officer elections under the supervision of the U.S. labor secretary, after former labor secretary Tom Perez alleged the union bent the rules in the most recent election, possibly affecting its outcome.

In a ruling filed Tuesday, U.S. District Judge George J. Hazel granted the Labor Department’s motion for summary judgment asking for new elections, saying Local 689 had failed to dispute the allegations against it.

The union, which represents more than 9,000 Metro employees, is in the midst of contract negotiations with the transit agency and is a key voice in efforts to revamp the troubled system’s finances and governance. As part of that effort, some elected officials are seeking an overhaul of the agency’s labor structure.

In the lawsuit, filed in June, 2016, under the federal Labor-Management Reporting and Disclosure Act, the Labor Department alleged that the union failed to provide adequate notice of its 2015 election, allowed members who were not in good standing to vote and run for officer positions, and approved “alternate, secret” policies that permitted some members to file late dues payments but not others — factors that impacted the election results, according to the suit.

In his ruling, Hazel ordered new elections for 22 of 40 officer positions, including executive positions such as president and first and second vice president, and key titles such as financial secretary-treasurer. The Dec. 2, 2015, vote had resulted in the reelection of Jackie L. Jeter as union president. She has held the office since 2007.

For “reasons stated in this Opinion, the Court shall declare the December 2, 2015, election held by Local 689, void … and directs the Union to conduct new elections for these offices under the supervision of the Secretary of Labor,” Hazel wrote.

The ruling came as a blow to Amalgamated Transit Union Local 689, which had argued that while it did not follow election rules “to the letter” it did not act in bad faith. The labor group said paying $300,000 to redo the vote would be an unfair punishment.

“We are currently reviewing the decision and looking into all of our options,” said David Stephen, spokesman for ATU Local 689. “Clearly, we are disappointed with the outcome.”

The Labor Department did not respond to a request for comment.

The union argued that the election came amid a massive effort to “modernize” its payment record system, which coincided in 800 members receiving past-due notices in October 2015.

The problem: Some members were allowed to enter into payment plans to cover their debts and restore their standing, while others weren’t given the same opportunity, according to the lawsuit.

“However, the option of entering into such a payment plan was not announced publicly to the Union membership,” Hazel wrote in his ruling.

The lawsuit named two members, Harry Johnson and Glenn Jarrett, whose candidacies were thwarted because they were more than a year late on dues payments. But Luis Chevalier, another member in a similar situation, was permitted to run, the filings say.

“The Union puts forth nothing to rebut this evidence that the election may have been affected by these violations,” Hazel wrote.

In total, wrote Hazel, at least 11 union members who were late on their payments were permitted to run for office; five were elected. The union requires officer candidates to have been in good standing for two consecutive years, meaning those who were late on their payments would not have been eligible to run.

Hazel also said the union failed to adequately inform members of the election, sending out notice only 14 days prior rather than the 15 days mandated by federal labor law and the union’s own bylaws. An investigation by the Labor Department found that at least 12 members weren’t notified of the election, which Hazel noted in his ruling was a large enough group to overcome the smallest margin of victory in the officer elections: 11 votes.

Stephen said the union plans to decide whether to file an appeal before Aug. 16 and to have the current officers remain in place until there is another election. “President Jeter looks forward to serving out her term,” he said.

The union had argued that some of its violations, such as sending out election notices late, were not made with malicious intentions.

“While the execution may have been slightly flawed, the intent was honorable,” the union said in a court filing defending its conduct.

Hazel rejected that line of defense.

“The ‘reasonableness of a union’s conduct’ is not a defense,” he said, citing legal precedent, “nor does a violation of [the federal Labor-Management Reporting and Disclosure Act] require a showing of bad faith or ill motive.”

Metro, which is currently in the midst of contract negotiations with Local 689, declined to comment on the ruling, calling it a union matter.

The union’s next election is scheduled for December 2018, and it was not immediately clear when a potential revote for the 2015 positions would take place. In issuing his ruling, Hazel noted that with the next election “nearly 18 months” away, he was not willing to simply have the labor secretary supervise that contest.

The U.S. Department of Labor said Wednesday night that it was pleased with the judge’s ruling. A timeline has not been set for the supervised vote, the department added, and union officers are expected to continue to serve in their current capacities until a new election is held.

This post has been updated.