Three men held at the Guantanamo Bay detention centre have been formally charged in connection with the 2002 Bali nightclub bombings and other plots in South-East Asia after 18 years in US custody.

But defence lawyers insisted afterwards the long-delayed process was so flawed it might have to be repeated.

The men returned to the secure courthouse encircled by razor wire on the US base in Cuba amid defence complaints about courtroom interpreters, that caused what was supposed to be a brief arraignment before a military commission into a two-day affair.

It was a rocky start to a case already expected to be complex because of the prolonged detention without charges for the three – an Indonesian and two Malaysians – and the brutal treatment they endured in CIA custody.

Encep Nurjaman, the Indonesian militant leader known as Hambali, and the two men face charges that include murder, terrorism and conspiracy before the commission, which is a hybrid of military and civilian law. They have not yet entered pleas.

The start of their long-delayed case comes as US President Joe Biden said he intends to close the detention centre, which holds 39 of the 779 men who were brought to the base following the September 11 attacks.

“Frankly, after this two-day arraignment, I didn’t see any evidence that he would get a fair trial,” said Christine Funk, the lawyer for one of the Malaysian defendants.

The defence complained the Malaysian interpreter’s language skills were so poor that at least one defendant couldn’t understand what was being said in court.

The defence also complained another Malay interpreter was improperly working for the prosecution because he previously assisted the prisoners when they appeared before a review board at Guantanamo.

The defence further complained the Indonesian interpreter had been overheard disparaging the men as terrorists who should be killed.

The judge, a Navy commander, allowed the proceeding to go on amid despite repeated objections.

Defence lawyer Brian Bouffard, who represents Malaysian defendant Mohammed Nazir bin Lep, said the arraignment was so flawed it should be done again.

“This one wasn’t done right,” Mr Bouffard said.

The trio is alleged to have been involved with the October 2002 suicide bombings of Paddy’s Pub and the Sari Club in Bali, Indonesia, and the August 2003 suicide bombing of the JW Marriott in Jakarta, Indonesia.

The attacks together killed 213 people, including 88 Australians.

-AAP