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In a new order Magistrate Judge James Marner acknowledged concerns of environmental groups that delaying the lawsuit while allowing construction to continue “would cause irreversible harm’’ both to the organizations that sued as well as to several imperiled species that would be affected by the new barrier.

But Marner said he also has to respect the arguments from the Justice Department, which is representing Homeland Security Secretary Kristi Noem, that its lawyers are legally prohibited from working while they are not being paid.

There are exceptions, the magistrate said, including “emergencies involving the safety or human life or the protection of property.’’ Absent those conditions, though, federal attorneys are are prohibited from working, “even on a voluntary basis,” he said.

“This court finds that under the current circumstances in this case, a stay is appropriate,’’ he wrote.

Work already has started on a 27-mile stretch through the grasslands of Southern Arizona’s San Rafael Valley. Conservation groups say the 30-foot steel bollards will interfere with the migration of jaguars and other animals.

The federal shutdown is unlikely to slow construction, which is being done not by federal workers but through a $393.5 million contract with Fisher Sand & Gravel Co., unaffected by the lack of a new federal budget.

The lawsuit filed by the Arizona Center for Biological Diversity and CATalyst contends the construction is illegal.

The plaintiffs want a court order to halt the project unless and until it complies with various environmental laws, something that becomes more difficult to do — and to undo — the more of the wall that is in place.

This may not wind up being the only legal fight with the Trump administration and its desire to build more border walls.

On Frday, Homeland Security along with U.S. Customs and Border Protection announced they had awarded 10 contracts totaling $4.5 billion to expand a “Smart Wall’’ system along the southwest border which includes barriers along with patrol roads, lighting, cameras, and detection systems. That list, the agencies said, includes $606 million for 23 miles of new secondary walls in the Tucson sector and another 66 miles of system features in Arizona.

The current lawsuit centers around a provision in the 1996 Immigration Reform and Immigrant Responsibility Act.

It authorizes Homeland Security to construct barriers and roads along the border. The Justice Department says it also allows Noem to waive any legal requirements that she, in her sole discretion, “determines necessary to ensure expeditious construction of the barriers and roads.’’

The lawsuit contends Congress acted illegally in 2005 when it amended the 1996 law, delegating the authority to waive laws to the secretary. Her attorneys dispute that contention.

Russ McSpadden of the Center for Biological Diversity said the delay in court action is unacceptable because of the speed at which construction is continuing.

“A few weeks ago, they had gotten about 350 feet up,’’ he said. “And then they hadn’t done anything for a few weeks.’’

And now, “They’ve tripled that,’’ McSpadden said. “So they’re full steam ahead now.’’

He said that endangers “one of the last, best wildlife corridors in the heart of the sky island ecosystem,’’ the valley bordered by the Patagonia and Huachuca mountains on the north and stretching far into Sonora.

“This is truly one of the best jaguar movement corridors we have remaining in the United States,’’ McSpadden said, saying three jaguars have used this corridor — and gone through where the fence is to be located — since 2015.

“Pronghorn also roam in this valley,’’ McSpadden said. “Few people know this, but porcupines live in this valley, bears cross here, mountain lions, coatimundi, javelina, you name it, this is one of the most spectacular wildlife corridors left.’’

It isn’t clear whether the magistrate’s delay necessarily means the case will sit idle, and wall construction will continue, no matter how long it takes for Congress to come up with a plan to fund the government and allow Noem’s lawyers to go back to work.

Marner noted that the government asked for — and he is granting — a stay only “until Department of Justice attorneys are permitted to resume their usual civil litigation functions.’’ If the government is still shut down at the end of the month, Noem’s attorneys must file a motion to keep the case on hold, he said.

Marner did not say whether he would grant a further stay at that time. McSpadden said that gives challengers a chance to once again present their arguments, though not necessarily to put the case back on the active calendar.

“We’ll argue pretty hard that if the case is stayed, then the wall needs to be stayed as well,’’ he said.

“We need to put all of this on pause,’’ McSpadden said. “There’s no reason that they should be able to get away with this, holding up our legal case while they just build full steam ahead.’’