Trump said the action by Colombian President Gustavo Petro jeopardised US national security and he has directed his administration to take retaliatory measures.
They include imposing emergency 25 per cent tariffs on all goods coming into the United States, which will go up to 50 per cent in one week.
He also promised a travel ban and visa revocations on Colombian government officials and its allies; fully imposing emergency Treasury, banking and financial sanctions and enhanced border inspections of Colombian nationals.
"These measures are just the beginning," Trump wrote on Truth Social.
"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 accused the US of treating the migrants like criminals.
In a post on social media platform X, Petro said Colombia would welcome home deported migrants on civilian planes, saying they should be treated with dignity and respect.
"The US cannot treat Colombian migrants as criminals," Petro wrote, noting that there were 15,660 Americans without proper immigration status in Colombia.
Los EEUU no pueden tratar como delincuentes a los migrantes Colombianos.— Gustavo Petro (@petrogustavo) Desautorizo la entrada de aviones norteamericanos con migrantes colombianos a nuestro territorio.EEUU debe establecer un protocolo de tratamiento digno a los migrantes antes que los recibamos nosotros.January 26, 2025
The United States is Colombia's largest trade and investment partner, the State Department says, and Colombia is also the US's third-largest trade partner in Latin America.
"Petro's finding out that tweets have consequences. He's not faced a US counterpart that looks at Colombia through a strategic lens, as a key ally, but as a country to make an example of," said Sergio Guzman, director of consultancy Colombia Risk Analysis, who added that financial sanctions could be potentially economically crippling.
Colombia's decision follows one by Mexico, which also refused a request last week to let a US military aircraft land with migrants.
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 late on Saturday condemned "degrading treatment" of Brazilians after migrants were handcuffed on a commercial deportation flight.
Upon arrival, some of the passengers also reported mistreatment during the flight, according to local news reports.
The plane, which was carrying 88 Brazilian passengers, 16 US security agents, and eight crew members, had been originally scheduled to arrive in Belo Horizonte in the southeastern state of Minas Gerais.
There, Brazilian officials ordered the removal of the handcuffs, and President Luiz Inácio Lula da Silva designated a Brazilian Air Force flight to complete their journey, the government said in a statement on Saturday.
The commercial charter flight was the second this year from the US carrying undocumented migrants deported back to Brazil and the first since Trump's inauguration, according to Brazil's federal police.
Officials from the US State Department, Pentagon, US Department of Homeland Security and US Immigration and Customs Enforcement did not immediately reply to requests for comment.
The use of US military aircraft to carry out deportation flights is part of the Pentagon's response to Trump's national emergency declaration on immigration on Monday.
In the past, US military aircraft have been used to relocate individuals from one country to another, like during the US withdrawal from Afghanistan in 2021.
This has been the first time in recent memory that US military aircraft were used to fly migrants out of the country, one US official said.
US military aircraft carried out two similar flights, each with about 80 migrants, to Guatemala on Friday.
