Colombia, America's third-largest trading partner in Latin America, swiftly responded, threatening a 50 per cent tariff on US goods.
Trump's punitive action appeared aimed at making an example of Colombia, the second case of a Latin American nation refusing US military deportation flights.
It was a demonstration of a more muscular US foreign policy and showed a renewed willingness by Trump to force other countries to bend to his will.
Colombian President Gustavo Petro says the US should treat migrant deportees with dignity. (AP PHOTO)
Trump wrote on Truth Social the refusal by Colombian President Gustavo Petro to accept the flights jeopardised US national security.
The retaliatory measures include imposing 25 per cent tariffs on all Colombian goods coming into the US, which will go up to 50 per cent in one week; a travel ban and visa revocations on Colombian government officials; and emergency treasury, banking and financial sanctions.
Trump said he would also direct enhanced border inspections of Colombian nationals and cargo.
"These measures are just the beginning," he 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!"
A US State Department spokesperson said visa processing had been suspended at the US embassy in Bogota in direct response to the decision not to accept deportation flights.
"The Department of State has suspended visa processing at US Embassy Bogota in direct response to President Petro's decision to not accept repatriation flights of Colombian citizens," the spokesperson said.
"Embassy Bogota has notified individual applicants who are affected. American Citizens Services will not be affected and will continue as normal."
US Secretary of State Marco Rubio says Colombia cancelled its authorisation of deportation flights. (AP PHOTO)
America will "no longer be lied to nor taken advantage of", US Secretary of State Marco Rubio said in a statement.
Rubio said Petro had authorised the deportation flights and provided all needed authorisations but then cancelled his authorisation when the planes were in the air.
A US official, speaking on condition of anonymity, said the military aircraft had departed California and were en route to Colombia when Bogota yanked the permissions to land.
The US president declared illegal immigration a national emergency and imposed a sweeping crackdown since taking office on January 20.
He directed the US military to help with border security, issued a broad ban on asylum and took steps to restrict citizenship for children born on US soil.
Colombia's Petro condemned the practice on Sunday, suggesting it treated migrants like criminals.
In a post on social media platform X, Petro said Colombia would welcome home deported migrants on civilian planes.
"The US cannot treat Colombian migrants as criminals," Petro wrote.
Petro said even though there were 15,660 Americans without legal immigration status in Colombia, he would never carry out a raid to return handcuffed Americans to the US.
"We are the opposite of the Nazis," he wrote.
Mexico also refused a request last week to let a US military aircraft land with migrants.
Trump did not take similar action against Mexico, the largest US trading partner, but has said he was thinking about imposing 25 per cent duties on imports from Canada and Mexico on February 1 to force further action against illegal immigrants and fentanyl flowing into the US.
The US is Colombia's largest trading partner, largely due to a 2006 free trade agreement, with $US33.8 billion ($A53.5 billion) worth of two-way trade in 2023 and a rare $US1.6 billion ($A2.5 billion) US trade surplus, according to US Census Bureau data.
Petro's comments add to the growing chorus of discontent in Latin America as Trump's week-old administration starts mobilising for mass deportations.
Brazil's foreign ministry on Saturday condemned "degrading treatment" of Brazilians after migrants were handcuffed on a commercial deportation flight.
Upon arrival, some passengers also reported mistreatment during the flight, according to local news reports.
