President Trump on Sunday night backed off a threat he had made earlier in the day to impose 25% tariffs and economic sanctions on Colombia, which the White House said had met its demands to repatriate migrants into the South American country.

Trump had issued the threat Sunday afternoon in retaliation for the Colombian government refusing to allow two military planes with migrants to land in the country. But after behind-the-scenes negotiations between the two countries, the White House announced that Colombia had “agreed to all of President Trump’s terms, including the unrestricted acceptance of all illegal aliens from Colombia returned from the United States.”

The tariff plans would be “held in reserve” unless the Colombian government didn’t honor the agreement, the White House said.

The move calls off what would’ve been Trump’s first use of tariffs since his inauguration last week, a decision that risked a trade war with a country that had enjoyed close economic relations with the U.S. for decades. Earlier in the day, Colombian President Gustavo Petro said he would hit back with his own tariffs on U.S. goods, promising to be uncowed by Trump’s duties and economic penalties and visa sanctions.

Luis Gilberto Murillo, the Colombian foreign minister, said: “We will continue to receive Colombians who are deported, guaranteeing them dignified conditions.”

The threat of tariffs against Colombia coincided with stepped-up deportation efforts around the country Sunday, dual events that marked a desire by the Trump administration to make early progress on one of his core campaign promises: cracking down on illegal immigration.

Authorities in several cities confirmed immigration actions Sunday, including Chicago, Los Angeles, Houston and Denver. U.S. Immigration and Customs Enforcement said authorities made 956 arrests on Sunday, a figure that appeared to be the highest daily tally ICE had announced since Trump began his second term.

The ordeal with Colombia began early Sunday morning, when Petro said on his X account that the “U.S. cannot treat Colombian migrants like criminals,” adding: “I disallow the entry of American planes with Colombian migrants to our territory.”

Two U.S. military C-17s had diplomatic permission to land in Colombia when they left San Diego carrying roughly 80 migrants each, a defense official said, but that authority was revoked Sunday en route. The planes then returned to the U.S., the official said.

Trump responded in a post on his Truth Social platform that the 25% tariffs would be raised to 50% in a week. Trump also said he was issuing a travel ban for Colombian government officials and visa sanctions on people connected to the country’s government.

“These measures are just the beginning,” Trump wrote. “We will not allow the Colombian Government to violate its legal obligations with regard to the acceptance and return of the Criminals they forced into the United States!”

Petro shot back defiantly in a long missive on X, threatening to respond in kind to Trump’s tariffs. “I am informed that you’ve imposed a 50% tariff on the fruits of our labor to enter the United States. I’ll do the same.”

Despite Petro’s statement, the Colombian government said there were “active conversations with the U.S. government, looking for agreements that assure minimum conditions of respect” for deported Colombians.

The tariffs and sanctions on Colombia were to be imposed under the International Emergency Economic Powers Act, a senior administration official said. That law grants the president broad authority to impose duties and penalties on other countries when he declares an economic emergency. The act hasn’t previously been used to impose tariffs, though President Richard Nixon used a precursor to the law to impose 10% tariffs on all imports in 1971.

The U.S. imported $16.1 billion in goods from Colombia in 2023, ranking it 26th, behind Sweden and ahead of Australia, among import partners, according to Census Bureau data. Crude oil accounted for roughly a third of that dollar value. Other top commodities the U.S. receives from Colombia include gold, coffee, bananas and fresh-cut roses.

In 2023, the U.S. accounted for 28% of the value of Colombia’s exports, more than any other trading partner, according to United Nations data. The U.S. sent $17.7 billion of goods to Colombia in 2023, giving the U.S. a slight trade surplus, with top commodities including light oils, corn, and civilian aircraft and parts, according to the Census Bureau.

Documents viewed by The Wall Street Journal showed that the Petro government had approved the arrival of the two military flights. Petro also said on X, before the flights, that two planes with deported Colombians would be arriving at 6:45 a.m. and 10 a.m. and his government would “receive them with flags and flowers.”

Later in the morning, Petro said on X that he had ordered the return of the planes, suggesting that he had done so because they were military aircraft and criticizing the use of handcuffs on the deported Colombians. “We will receive our countrymen on commercial planes, without them being treated like criminals,” he wrote. Just minutes after Trump said he would impose tariffs, Petro’s office said the government would make the presidential plane available to ferry back the Colombians who were to have been deported Sunday.

The White House statement said Colombia had agreed to accept the transport of migrants in military aircraft. Despite holding fire on the tariffs, the White House added that visa restrictions would “remain in effect until the first planeload of Colombian deportees is successfully returned.”

The U.S. had been deporting migrants to Colombia and other Latin American countries under the Biden administration, usually using commercial flights, the senior State Department official said. So far in January, there have been 90 deportation flights, with 48 to Guatemala and Honduras, 14 to Mexico and eight to Colombia, said Witness at the Border, a U.S. immigration advocacy group that tracks flight data.

Petro on X sought to cast Trump’s tariff threat as an affront to his country’s freedom. “You don’t like our freedom—fine. I do not shake hands with white slaveholders,” Petro said, adding later: “You will never dominate us.”

The dust-up with Colombia reflects the discontent in some Latin American capitals, many of them run by leftist presidents, with the new administration in Washington. Brazil’s foreign ministry issued a statement Sunday protesting what it said was “degrading treatment” of Brazilians deported from the U.S., some of whom it said were handcuffed around their hands and feet on a plane heading for the country Friday.

Trump has vowed to carry out the largest mass deportation in U.S. history, with his team targeting immigrants in the country illegally with criminal backgrounds, including some minor offenses.

Trump’s planned raids have caused fear among migrants , including in progressive sanctuary cities such as Chicago . Some migrants who haven’t fled those cities have said they have been scared to go to work or send their children to school. Trump border czar Tom Homan and Acting Deputy Attorney General Emil Bove were in Chicago on Sunday to oversee migrant arrests.

Federal agents from across the Justice Department were working with Homeland Security officers on an immigration crackdown in Chicago that Bove called “a critical mission to take back our communities.”

In an unusual move for a senior Justice Department official, Bove personally observed the operation in Chicago. He watched the first arrest, of “an illegal immigrant who remained in the country despite having killed a 19-year-old woman while driving under the influence,” a Justice Department official said, without providing the person’s name.

Agents from the U.S. Bureau of Alcohol, Tobacco, Firearms and Explosives, the Federal Bureau of Investigation, the Drug Enforcement Administration and U.S. Marshals Service, whose work rarely includes immigration enforcement, were involved in the operation after Trump gave them power last week to help carry out deportations.

Write to Alyssa Lukpat at alyssa.lukpat@wsj.com , Juan Forero at juan.forero@wsj.com and Sadie Gurman at sadie.gurman@wsj.com