The US government intends to hand over to a third country an American citizen captured in Syria allegedly fighting for the Islamic State group, rather than present him to the US justice system, a court filing showed Tuesday.

In the Trump administration's first decision on how to deal with citizens caught fighting for a designated terror group, the US military plans to turn over the man, a dual US-Saudi citizen born in the United States and now held in Iraq, to an unnamed country as early as late Thursday.

The American Civil Liberties Union, which has been representing the man, known in court documents only as "John Doe", said it plans to ask the court to block the transfer, arguing that he has not been charged with a crime and has the right to due process under US laws.

"The Trump administration has been detaining this American citizen unlawfully for more than seven months, and forcibly rendering him to another country would be an unconscionable violation of his constitutional rights," said ACLU attorney Jonathan Hafetz.

"He should either be charged or freed, not handed over to an unnamed foreign government."

The notice was made in a sealed two-page filing to the federal district court in Washington DC late Monday. A heavily redacted version of the filing was released Tuesday, saying the government had bowed to the court's requirement that it give a 72 hour notification before it intends to transfer the detainee.

The country he will be transferred to was blacked out in the public document. The government has earlier said it has two countries he could be sent to; one is widely presumed to be Saudi Arabia, the second could be Iraq.

The man is the only known US citizen held as an alleged enemy combatant from the battlefields of Iraq and Syria.

On September 14 the Pentagon confirmed that they were holding him, saying he had been fighting for the Islamic State group and surrendered to the allied Syrian Democratic Forces in Syria days earlier.

He was moved to Iraq where he has been interrogated by military and FBI investigators. The International Committee of the Red Cross was given access to him, and the ACLU sued to be able to represent him.

In subsequent discussions with him, the ACLU says he asserted his habeas corpus rights to be charged under US law or be freed.

It's not clear why the government refuses to hand him over to the US justice system, as other Americans accused of terrorism have been.

But analysts think the Trump administration wants to avoid the fundamental question of whether an American caught fighting for Islamic State has any rights.

Between 100 to 200 US nationals traveled to Syria and Iraq after 2010 to work and fight in their ranks, according to various estimates.

A handful are known to have been killed, but the number isn't clear: the US has not provided any data.

Iraq and Syria's Kurds are holding a large number of captured IS "foreign fighters", including some with European nationality. Most of their home countries don't want them, posing a dilemma that US Defense Secretary Jim Mattis said in February was "an international problem."

Trump has pledged to be tough on any US jihadists, threatening to send them to the military prison at Guantanamo Bay, Cuba, where 41 non-American detainees are held.

But rights lawyers say that putting "John Doe" in Guantanamo would also violate his rights as a citizen.

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