A federal judge in San Francisco on Tuesday put a temporary freeze on part of President Donald Trump’s executive order threatening to withhold federal funds to cities and counties that thwart federal immigration officials.

Cracking down on so-called “sanctuary” jurisdictions was one of the most important parts of an executive order signed by the president in January.

“It’s not surprising … The decision is within line with everything that the federal courts have done with respect to what Trump is trying to do.”

U.S. District Judge William Orrick granted a temporary order in favor of San Francisco and Santa Clara Counties, which challenged the sanctuary jurisdiction provision of the order.

“The counties have demonstrated that they are likely to succeed on the merits of their challenge … that they will suffer irreparable harm absent an injunction, and that the balance of harms and public interest weigh in their favor,” wrote Orrick, whom former President Barack Obama appointed to the bench.

Orrick wrote that the counties would suffer irreparable harm if they lost federal funding and that the executive order does not define “sanctuary jurisdiction,” leaving it to the discretion of the homeland security secretary and the attorney general. The language of the order effectively would place new conditions on cities and counties not placed by Congress, according to the ruling.

“That said, this injunction does nothing more than implement the effect of the government’s flawed interpretation of the order,” Orrick also wrote. “It does not affect the ability of the attorney general or the secretary to enforce existing conditions of federal grants or 8 U.S.C. 1373, nor does it impact the secretary’s ability to develop regulations or other guidance defining what a sanctuary jurisdiction is or designating a jurisdiction as such.”

Dale Wilcox, executive director of the Immigration Reform Law Institute, said his reading of the ruling is that the Department of Homeland Security and Department of Justice could still withhold funds on three specific programs — the State Criminal Alien Assistance program, the Justice Assistance Grant program, and the Community Oriented Policing Services program.

White House chief of staff Reince Preibus told reporters that the administration would appeal. The Justice Department, in a prepared statement, indicated that it would take action against sanctuary jurisdictions as permitted by law.

“The Department of Justice previously stated to the Court, and reiterates now, that it will follow the law with respect to regulation of sanctuary jurisdictions,” the statement read.

Orrick wrote that Trump’s executive order and public statements by the president and Attorney General Jeff Sessions went far beyond that in scope, potentially threatening all federal funding. For Santa Clara, that would be as much as $1.7 billion. For San Francisco, it could be as much as $1.2 billion. The judge wrote that those funds could not be touched without a change by Congress unless the statutes specifically authorized those moves.

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Joseph Guzzardi, a spokesman for Californians for Population Stabilization, said he was disappointed that the judge placed any restrictions on the administration’s ability to punish sanctuary cities. He compared it to judicial orders holding up Trump’s temporary ban on travelers from a group of terrorism-compromised countries.

“It’s not surprising,” he said. “The decision is within line with everything that the federal courts have done with respect to what Trump is trying to do.”

Orrick noted that at a court hearing earlier this year, Justice Department lawyers explicitly disavowed the ability of the executive order to add conditions to grants not authorized by Congress. But he wrote that the language of the executive was much broader than the interpretation offered by government attorneys.

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“The defunding provision is entirely inconsistent with law in its stated purpose and directives because it instructs the attorney general and the secretary to do something that only Congress has the authority to do — place new conditions on federal funds,” the order states.

Orrick wrote that the executive order does not clearly define “sanctuary jurisdictions” and does not spell out clearly exactly what jurisdictions must do to keep their funding.

The judge also wrote that any funds withheld from local jurisdictions must have a “nexus” to immigration enforcement.

“Federal funding that bears no meaningful relationship to immigration enforcement cannot be threatened merely because a jurisdiction chooses an immigration enforcement strategy of which the President disapproves,” he wrote.