President Trump announced a new emergency 5% tariff on all goods imported from Mexico, saying it was the only way to get America’s southern neighbor to step up and do more to stop the flow of migrants.

The tariffs will take effect June 10, and will increase to 10% on July 1, 15% on Aug. 1, and so on up to 25%, until the situation is resolved.

The president cast the move as a humanitarian urgency.

“Gang members, smugglers, human traffickers, and illegal drugs and narcotics of all kinds are pouring across the southern border and directly into our communities,” he said in a statement. “Thousands of innocent lives are taken every year as a result of this lawless chaos. It must end NOW!”

Mr. Trump said he’s using his authority under the International Emergency Economic Powers Act.

That the border is in crisis became clear this week after authorities announced the largest-ever group of migrants. Some 1,036 people — most of them unaccompanied children or families — breached the wall in El Paso on Wednesday.

Borderwide, some 4,500 people are being caught every day, putting the country on track for another record month in May, said Homeland Secretary Kevin K. McAleenan.

He said a record 80,000 migrants are also in custody right now, with the numbers so overwhelming that the government can’t process them fast enough, and no longer has space to put them.

Mr. Trump’s move reflects a simmering dissatisfaction by Trump administration officials with Mexico, which at times has talked tough, but failed to come up with policies to stop the flow of tens of thousands of Central American migrants traversing its territory each week — most headed for the U.S.

“Mexico must step up and help solve this problem,” the president said. “We welcome people who come to the United States legally, but we cannot allow our laws to be broken and our borders to be violated. For years, Mexico has not treated us fairly — but we are now asserting our rights as a sovereign nation.”

The tariff announcement comes just after the president canceled another set of tariffs on steel and aluminum imports from Mexico, which was a precondition to pursuing action on the new U.S.-Mexico-Canada trade deal that Mr. Trump had worked out to replace the North American Free Trade Agreement.

It’s not clear whether the tariffs will scuttle that trade deal, but acting White House Chief of Staff Mick Mulvaney said the administration considers the issues separate.

He said, though, that Mexico can quickly solve matters.

“They have some of the strongest immigration laws in their country. We fully believe they have the ability to stop people coming in on their southern border,” Mr. Mulvaney said.

Mr. McAleenan said Mexico stops only about one-fifth of migrants coming across its own southern border, and most of those are headed to the U.S.

He said there are three big things Mexico could do: target the smuggling cartels that control the flow of people; stop more people at Mexico’s southern boundary; and sign a first-safe-country agreement, which would mean the Central Americans lodging asylum claims in the U.S. could be sent back to Mexico.

Mr. Trump did not set targets Mexico needed to reach to head off the tariffs, but Mr. Mulvaney said it must be a serious drop.

“That number needs to start coming down, immediately,” he said.

The White House said it briefed Republicans on Capitol Hill, some of whom raised questions about the legality of using the economic powers act for this purpose. The administration said it felt it was on firm legal footing.

Mr. Trump, in his statement announcing the tariffs, said he also expects action from Congress to do more to close the legal “loopholes” that migrants are exploiting to gain a foothold in the U.S.

“When that happens, the measures being announced today can be more readily reduced or removed,” he said.

Smuggling cartels are aware of those loopholes, which virtually guarantee adults who cross the border with their children will be released into the U.S. rather than quickly deported. Once in the U.S. they can usually get work permits and gain a foothold here, then not show up for any eventual deportation hearings.

Mr. McAleenan, who was traveling in Guatemala this week to get a firsthand look at the problem, said a man there summed it up: “A child is like a passport for migration.”

That was likely the enticement behind Wednesday’s record group, according to a Customs and Border Protection official who briefed reporters.

Of the people in the group, 63 were deemed to be children traveling unaccompanied by a parent, while 934 came as parents or children traveling together as families.

The group was so large that it took five minutes to cross, and agents were still processing them Thursday afternoon.

The previous record for Central American migrants had been groups of between 400 and 500.

Such groups were relatively unheard of until the last year or so, when smuggling cartels began to organize the massive numbers.

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