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Kilmar Abrego Garcia has been taken into custody after arriving at a US Immigration and Customs Enforcement (ICE) office in Baltimore.
In a statement, Secretary of Homeland Security Kristi Noem confirmed his arrest and said that ICE "are processing him for deportation".
He was mistakenly deported to a notorious prison in El Salvador in March, and then brought back to face criminal charges.
US authorities have informed him he may be deported to Uganda, following his refusal to accept a plea deal, his lawyers say.
His legal team accuses the US of trying to "coerce" him to plead guilty by threatening to re-deport him "halfway across the world".
"The only reason that they've chosen to take him into detention is to punish him, to punish him for exercising his constitutional rights," one of his attorneys, Simon Sandoval-Moshenberg, told reporters outside the ICE office.
He said that Mr Abrego Garcia had filed a new federal lawsuit in Maryland challenging his current detention and potential deportation "to Uganda or any other country" until he has a trial.
They have said their client declined an offer to plead guilty to human smuggling charges in exchange for deportation to Costa Rica. He was asked to check in on Monday at the field office in Baltimore.
During the interview, Mr Sandoval-Moshenberg said ICE officers had taken Mr Abrego Garica into custody with no explanation. An officer told the attorneys he would be taken to a detention center but would not specify which one.
His attorney argued there was no reason to detain Mr Abrego Garcia, as he was under ankle monitoring and "basically on house arrest".
His supporters now fear he faces a second deportation - this time to Uganda, a country where he has no known ties.
Supporters held a rally outside the premises in support of the Salvadorean national, whose drawn out immigration case has made global headlines.
In a statement, Ms Noem alleged Mr Abrego Garcia was guilty of human trafficking and domestic abuse. President Donald Trump would not allow him to "terrorise American citizens any longer".
The US reached bilateral deportation agreements with Honduras and Uganda as part of the Trump crackdown on illegal immigration.
Documents obtained by CBS News, the BBC's US partner, quote Uganda's foreign ministry as saying it prefers individuals it accepts to be from African countries.
The saga of Mr Abrego Garcia's deportation case has been in the news since March when he was deported to his native El Salvador, and initially kept in the notorious Cecot prison.
But after US government officials acknowledged he was deported due to an "administrative error", a judge ordered the administration to facilitate his return.
He was sent to Tennessee where he was charged in a human smuggling scheme and detained until his release on Friday after a ruling by a federal judge.
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