A federal judge on Friday rejected the Trump administration’s new regulations designed to expand the government’s ability to detain migrant children who enter the United States illegally, often to seek asylum with their parents.

The move to supplant a decades-old legal agreement that set strict limits on the incarceration of such children with new government policy was part of a wider campaign by the Trump administration to discourage migrant parents from journeying with their children to the southern border.

Judge Dolly Gee of the Federal District Court in Los Angeles, who oversees the 1997 court settlement known as the Flores agreement, concluded that the administration’s attempt to frame regulations that would carry out the mandate to protect migrant children — but allow them to be detained for long periods — was not adequate.

Under the consent decree, the government must seek to expeditiously release children from detention, a requirement that has been interpreted to mean that they must not be held longer than about 20 days.

“The Flores Settlement Agreement remains in effect and has not been terminated,” Judge Gee, an appointee of President Barack Obama, wrote in a two-page order.

She said the new regulations “fail to implement and are inconsistent with” the terms of the agreement, which the government must now continue to comply with.

The new regulations were an attempt to end more than 20 years of court oversight on migrant children’s detention.

Unveiled on Aug. 21, they would terminate the court’s review of facilities holding children and eliminate a requirement that such facilities be licensed by whatever state they are in, as well as remove the 20-day limit on how long children can be held in a secure facility.

“The Department of Justice is disappointed that the court is continuing to impose the outdated Flores Agreement even after the government has done exactly what the Agreement required: issue a comprehensive rule that will protect vulnerable children, maintain family unity, and ensure due process for those awaiting adjudication of their immigration claims,” a department spokesman said in a statement.

Administration officials had said that the new regulations would fulfill the Flores agreement’s provisions for ensuring that children in the government’s custody are “treated with dignity, respect and special concern for their particular vulnerability.”

But lawyers for the groups who sued on behalf of migrant children said that they did not fulfill the requirements of the settlement. If adopted as written, they warned in court filings, the new rules would “strike a mortal blow to crucial rights and protections that the settlement confers on vulnerable children.”

After the ruling, Carlos Holguin, who has litigated the case since filing a class-action lawsuit in 1985, said, “We are gratified that the court has ruled in the way it has to protect children from the worst excesses of immigration-related detention.”

The administration claims that the Flores agreement has created incentives to illegal immigration by essentially giving a free pass into the United States to migrants who arrived at the border with a child. This Flores “loophole,” officials argued, led to a rise in the number of families crossing the southern border in recent years.

More than 450,000 people traveling as members of a family have crossed the border in the current fiscal year that ends Sept. 30, or about three times as many as last year.

The Flores agreement has its origins in a class-action lawsuit filed in 1985 against the federal government over its treatment of migrant children in federal detention facilities, including a 15-year-old Salvadoran girl named Jenny Flores and a 12-year-old girl named Alma Cruz. In 1997, immigration officials in the Clinton administration agreed to settle the lawsuit, establishing the standards for the detention of minors.

Flores lawyers have returned to court dozens of times in recent years to compel the government to abide by the settlement’s provisions, often after dispatching legal and medical teams to inspect conditions and interview children at detention centers.

President Trump has made combating illegal immigration his signature issue, and the large influx of families, mainly from Central America, has made it difficult to fulfill his promise to secure the border.

In June 2018, Mr. Trump signed an executive order instructing the Justice Department to “promptly” request that the federal court alter the agreement. That order followed the president’s decision to stop taking children from parents at the southern border, a policy that drew widespread condemnation.

Judge Gee refused. She blamed more than 20 years of congressional inaction and “ill-considered executive action” for the “current stalemate.” Three months later, the administration published the proposed new Flores regulations for public comment. In August, it published a final version in the Federal Register and said they would take effect in 60 days, barring a court ruling against them of the kind that Judge Gee just issued.

The Obama administration, which faced a new spike in migrant families arriving on the border in 2014, tried and failed to get out from under the agreement. The Obama administration had erected family detention centers with the aim of holding families until their court cases were completed, a period that almost always stretches well beyond the 20-day limit.

But in 2015, Judge Gee expanded the scope of the settlement to clarify that it applied not just to children traveling alone, but also to those who crossed the border with their parents, ending prospects for long-term family detention.

In addition to trying to update detention standards for migrant children, the Trump administration recently has taken several steps to make it more difficult for migrants to enter the United States.

It has signed agreements with Mexico, Guatemala, Honduras and El Salvador to encourage those countries to absorb more migrants who are seeking asylum and has introduced a policy that disallows asylum petitions from migrants seeking protection in the United States unless they have sought and failed to obtain protection from the first country through which they pass en route. The administration has also forced more than 45,000 people to wait in border towns in Mexico for their court dates in the United States.

The government currently operates three family detention centers with a 3,000-person capacity.

Kevin McAleenan, the acting Homeland Security Secretary, said on Sept. 25 that the administration would roll out new measures to end what he called “catch and release.” Migrant families who do not express a fear of persecution in their home countries could be swiftly deported, and more people who requested asylum would be sent back to Mexico to await their hearings, officials said.

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