US NAVAL BASE AT GUANTANAMO BAY, Cuba — A pre-trial hearing for an alleged Al-Qaeda operative accused of masterminding the attack on the USS Cole resumed Wednesday behind closed doors and without the defendant in a US military tribunal -- amid protests from his lawyers and media outlets.

The session at the US naval base at Guantanamo Bay, Cuba is the first of its kind under the administration of President Barack Obama.

Abd al-Rahim al-Nashiri, a Saudi citizen, faces the death penalty for the bombing of the US Navy destroyer off Yemen in October 2000 that left 17 sailors dead and a 2002 attack on the French oil tanker MV Limburg that left one dead.

"It's really an unprecedented situation, this is the first time that I go to a hearing without my client," defense lawyer Richard Kammen, who has worked on 35 death penalty cases, told reporters.

Following an initial day of deliberations Tuesday, lawyers and prosecutors were expected to take up the sensitive question of Nashiri's detention in secret CIA prisons and the possible mistreatment he allegedly suffered there between 2002 and 2006 before being transferred to the US-run prison in Cuba.

Prosecutor Joanna Baltes said Nashiri, 47, was not allowed to attend the session because of the classified nature of information to be taken up -- an explanation met with dismay by another member of his defense team.

"Mr Nashiri has a statutory right to be present at all sessions of the military commissions," said lawyer Steve Reyes.

Fourteen media outlets had previously protested the secret session in a petition to the tribunal being overseen by Judge James Pohl, who said Tuesday he wanted to "minimize the closure."

Pohl explained that during the secret session, two sealed demands by the defense -- calling for more information on the condition surrounding Nashiri's arrest and detention -- would be taken up.

Kammen said the defense had received 12,000 pages of classified documents in addition to 40,000 declassified ones.

But "what we're getting is nothing compared to what we'd expect," he said, adding that he was not able to discuss anything involving the CIA.

The closed part of the proceedings was also expected to focus on DNA samples and fingerprints taken at the attack sites, as well as statements made by the accused during his detention, in order to decide what should remain classified.

Anthony Mattivi, another prosecutor, said during Tuesday's session that the government intended to use some of Nashiri's statements against him.

But chief prosecutor Mark Martins told reporters that the law on military tribunals forbids the use of testimony obtained by coercion.

Martins said Wednesday's closed session was the first since he took up his post in 2011 and since military tribunals resumed under Obama.

Kammen meanwhile said nothing had really changed since 2006 when military tribunals were first reformed under the administration of George W. Bush.

"The system is not any more open, transparent and fair," he said.

Despite the protests, Pentagon spokesman Todd Breasseale said sessions open to the press would only resume Thursday.

Nashiri's trial is not expected to begin in November, according to Pohl.

Al-Qaeda claimed responsibility for the suicide attack on the USS Cole, which saw militants riding an explosives-laden skiff blow a 30-by-30-foot (10-by-10-meter) hole in the ship.