The Education Department is reviewing the ruling, said Liz Hill, a spokeswoman.

Judge Moss’s decision may lead to changes in how the government handles tens of thousands of existing claims from students seeking to have their loans discharged. But any remedies he orders may soon be blunted: The Education Department is working to completely revise its system for handling future requests.

Even so, the ruling was the latest in a series of judicial rebukes to the Trump administration for trying to shortcut the government’s formal process for adopting and eliminating agency rules. Judges have rejected attempts by multiple agencies to eliminate or indefinitely suspend rules they disliked, including new restrictions on methane emissions from oil and gas wells and an immigration pathway for entrepreneurs running technology start-ups.

The loan forgiveness system, known as borrower defense, was created in 1995 but was little used until a few years ago, when a series of failures at for-profit chains like Corinthian Colleges and ITT generated a flood of claims from borrowers seeking relief from large debts incurred for credentials that did little to advance their job prospects.

At the end of last year, the Education Department had nearly 100,000 claims queued up, and many of them had languished for years without a decision. Ms. DeVos suspended a rule change set in motion by the Obama administration that would have granted quicker relief to large batches of defrauded borrowers. It also would have required troubled schools at risk of generating claims to put up financial collateral.

At a conference last year, Ms. DeVos criticized that approach.

“While students should have protections from predatory practices, schools and taxpayers should also be treated fairly as well,” she said. “Under the previous rules, all one had to do was raise his or her hands to be entitled to so-called free money.”