Somali man taken to New York to face criminal court trial after being questioned for two months without a lawyer

The Obama administration approved the secret detention of a Somali terror suspect on board a US navy ship, where for two months he was subjected to military interrogation in the absence of a lawyer and without charge.

The capture and treatment of Ahmed Abdulkadir Warsame has rekindled the debate within the US about the appropriate handling of terror suspects. Republicans in Congress have objected to Warsame being brought to New York this week to be tried in a criminal court – an attempt by the Obama administration to avoid sending the prisoner to Guantánamo Bay, which it has promised to close.

From the opposite viewpoint, civil rights groups have objected to the secret questioning of Warsame on board a navy vessel, an innovation that they fear could see a new form of the CIA's widely discredited "black site" detention centres around the world.

There is some evidence that the US government is turning to detention at sea as a way of avoiding legal and political impediments in the treatment of terror suspects, both domestically and on the international stage.

Last week Admiral William McRaven, soon to become head of US Special Operations Command, told his confirmation hearing that militants captured outside Afghanistan were often "put on a naval vessel" to be held until they could be sent to a third country or a case was compiled against them for prosecution in the US courts.

Legal documents show that Warsame was captured on 19 April on a boat between Yemen and Somalia. Administration officials told the Washington Post that they had intercepted the boat after being given information that it might be carrying important terrorists.

Warsame was flown to New York on Monday and now faces nine charges, including conspiracy and providing support to two groups closely monitored by the US: the militant Somali group al-Shabab and al-Qaida in the Arabian Peninsula in Yemen. He is also accused of weapons offences including conspiracy to teach and demonstrate the making of explosives, and having been given military training by the al-Qaida group.

Warsame, who faces life in prison if convicted, has pleaded not guilty to all charges.

Officials told the Washington Post that Warsame was interrogated on "all but a daily basis" on board the ship. The rules governing the questioning were those set out in the army field manual which prohibit controversial techniques used by the CIA after 9/11 such as waterboarding.

But the right to a lawyer was withheld along with other habeas corpus rights known in the US as Miranda rights. Officials claimed Warsame did not need to be given those because he was being interrogated for intelligence purposes rather than in preparation for his prosecution.

Civil rights groups have said the secret interrogation was a blatant violation of the Geneva conventions that prohibit prolonged detention of suspects at sea. Article 22 of the third Geneva convention states that combatants can be kept at sea only for as long as needed to transfer them to land.

Had Warsame been taken to Guantánamo, he would have immediately been entitled to a lawyer and to benefit from the other rights that were withheld from him on board the ship.

Wells Dixon, a senior lawyer at the Centre for Constitutional Rights who has represented several Guantánamo detainees, said the Obama administration, like the Bush one before it, was selectively borrowing principles from the laws of armed conflict. "And it is always to the detriment of the detainee."

Officials in Washington said they gave Warsame a four-day "break" from interrogation to separate the intelligence from the criminal part of his questioning. The intelligence portion, they said, had been "very, very productive".

After the interlude, he was questioned with an eye to preparing a criminal case against him. At this stage he was read his rights before each session, though officials said he waived them voluntarily.

The justice department hopes this separation will avoid legal difficulties further down the line. Specifically, it wants to prevent crucial information being deemed inadmissible to the New York criminal courts on the grounds that it was obtained from the defendant without his having been given his full rights.

But Dixon said the distinction between portions of the interrogation was spurious. "We know from experience representing detainees in Guantánamo that it is very easy to break an individual who is held incommunicado. It is, by contrast, very, very difficult to undo the damage, so providing a person with a 'few days off' in no way establishes that they voluntarily waived their rights."

Leading Republicans have also objected to the handling of Warsame, accusing the Obama administration of attempting to bypass the will of Congress.

The Republicans have blocked the transfer of detainees in Guantánamo for trial in civilian courts on the US mainland, claiming that to import terror suspects poses a risk to the American public. "The administration has purposefully imported a terrorist into the US and is providing him all the rights of US citizens in court," said Mitch McConnell, leader of the Republicans in the Senate. "This ideological rigidity being displayed by the administration is harming the national security of the United States of America."