President Trump said Thursday that he wouldn’t pay for the California National Guard to join his deployment to the border, saying Gov. Jerry Brown’s restrictions meant the troops would “do nothing.”

Hours later the Pentagon undercut Mr. Trump, telling California that the deployment is on track and the government will still pick up the tab for the 400 troops Mr. Brown has ordered mobilized.

It’s the latest twist as the president tries to get more help for Homeland Security on his own terms, and finds himself once again battling California, which has its own ideas about how to handle illegal immigration.

Mr. Brown signed an order Wednesday saying his troops will help Customs and Border Protection, the Homeland Security agency responsible for the border, with catching drug smugglers, nabbing human traffickers and combatting criminal gangs. But he doesn’t want them to do anything that would be seen as policing illegal immigration.

Mr. Trump tweeted that it wasn’t good enough.

“Governor Jerry Brown announced he will deploy ‘up to 400 National Guard Troops’ to do nothing,” the president tweeted. “The crime rate in California is high enough, and the Federal Government will not be paying for Governor Brown’s charade. We need border security and action, not words!”

The governor’s office, though, pointed to Homeland Security Secretary Kirstjen Nielsen, who’d signaled the California offer was acceptable.

And by Thursday afternoon, just two hours after Mr. Trump’s vow not to pay for the deployment, the National Guard said it would fund the operation.

“We received written confirmation from the Pentagon that it’ll continue to fund the [California Guard] mission,” the state guard said. It said the payment is consistent with the terms and restrictions Mr. Brown announced in his order Wednesday.

Neither Homeland Security nor the White House was able to shed light on Mr. Trump’s tweet or the guard’s decision to move ahead anyway.

The striking part about the brouhaha is that Mr. Brown’s decision to deploy the guard would normally appear to be a victory for Mr. Trump. Many immigrant-rights advocates and Mr. Brown’s fellow Democrats in the state didn’t want to see any guard commitment.

And drug and human trafficking are both run by the cartels that control the illegal immigrant routes through Mexico, so assisting the Border Patrol in those missions could make a dent in illegal immigration as well.

Mr. Trump himself recognized the scope of the problem while touring a Coast Guard facility in Florida with Ms. Nielsen on Thursday.

“Human trafficking is worse than it’s ever been in the history of this world,” he said. “Drugs are flowing into our country. We need border protection; we need the wall. We have to have the wall.”

He blamed Democrats for stymying his efforts.

California Lt. Gov. Gavin Newsom, who is running to succeed the term-limited Mr. Brown in this year’s election, was defiant In the face of Mr. Trump’s complaints. He said the president should focus on illegal immigrant Dreamers and “comprehensive immigration reform” instead of deploying the guard.

“Work on those things and get back to us,” he tweeted in reply to the president.

Mr. Trump, though, said he saw “a little bit of a revolution” in California from communities balking at the state’s refusal to assist on illegal immigration.

He praised San Diego County “for defending the rule of law and supporting our lawsuit against California’s illegal and unconstitutional ‘Sanctuary’ policies.”

“California’s dangerous policies release violent criminals back into our communities, putting all Americans at risk,” the president tweeted.

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