Professional investigators who deplored torture were repeatedly sidelined as CIA and soldiers with little training took harsh steps

One of the biggest and most explosive clashes at Guantánamo Bay has been fought not between guards and prisoners but between US interrogators, the leaked files reveal.

It was a fundamental clash of cultures: between those who stuck rigidly to US law and those who, in the frightening post-9/11 world, adopted techniques from a US manual detailing psychological and physical torture used by China during the Korean war.

In theory there was – and still is – a simple command structure at Guantánamo, run by the commander of the Joint Task Force Guantánamo (JTF GTMO in military jargon). But in reality there were lots of agencies at the naval base in Cuba, sometimes working together but more often at odds and at times barely speaking.

On the ground alongside the JTF GTMO interrogators were the Criminal Investigative Task Force (CITF), an elite unit, many of whose members had a law enforcement background and opposed the use of harsh methods.

Also in the mix was the CIA, which George Bush made the lead agency in spite of its failure to stop 9/11. Jostling for a piece of the action were the FBI and the Behavioural Science Consultation Team, a group of psychiatrists and psychologists set up by the defence department. The files confirm that interrogators were also present from foreign intelligence services.

The battles being fought on the ground mirrored the debate and power plays in Washington, as figures such as Bush, his vice-president, Dick Cheney, defence secretary Donald Rumsfeld, national security adviser Condoleezza Rice and secretary of state Colin Powell argued over the ethics and legality of what was happening at the naval base.

The first Guantánamo detainees arrived on 11 January 2002. Rumsfeld ordered the US Southern Command – based in Miami and responsible for Latin America and the Caribbean – to take responsibility for guarding the detainees and oversee interrogation. Southern Command on 16 February gave this role to JTF-170, which eventually became JTF GTMO.

Evidence of the in-fighting among the agencies can be found towards the end of the detainee reports, in which the camp commander assesses the risk posed by a prisoner and his intelligence value. The commander makes a recommendation whether to release, keep in detention or send to another government for imprisonment.

The final paragraph deals with "co-ordination" between the agencies and it is here that the friction surfaces. The commander often reports that CITF "defers" to JTF GTMO. "Defers" sounds dull and bureaucratic but it is a loaded word in the context of Guantánamo, reflecting a profound difference in interrogation techniques and conclusions.

Typical is a report on Saleh Abdall al-Oshan, a Saudi who was among the first to arrive at Guantánamo, on 21 January 2002. The JTF GTMO assessment, written in 2004, was that "this detainee is a member of al-Qaida and/or its global terrorist network". But the commander added: "CITF assessed the detainee as a low risk on 22 March 2004. In the interest of national security and pursuant to an agreement between the CITF and JTF GTMO Commanders, CITF will defer to JTF GTMO's assessment that the detainee poses a medium to high risk."

Time and time again CITF is at odds with JTF GTMO but forced to defer.

CITF, whose members are drawn from the army, navy and air force, is part of the defence department and is based at Fort Belvoir, near Washington. Its approach to interrogation was to try to befriend prisoners, chat to them over tea, win their confidence and build up information gradually. Some members of the team eventually went public, in television interviews and Senate hearings, saying that harsh interrogation techniques made cases unprosecutable and were counterproductive in any case, pushing detainees into cocoons of silence.

By contrast, JTF GTMO is made up of troops from a traditional military background. They saw their mission as primarily intelligence-gathering rather than constructing a legal case. Again, in the case of Oshan, the commander's report emphasises he was transferred to Guantánamo in hopes of providing intelligence. "Detainee may provide information on the refugee camp outside Spin Buldok, AF [Afghanistan], and Islamic presence in the Philippines," the report says.

Over and over again the stress in the reports is on intelligence-gathering.

Some of the troops transferred to JTF Guantánamo had no background in interrogation. Among the first were a group from Fort Huachuca, Arizona. They had had six weeks of training in how to withstand torture – very different from conducting interrogations.

The military used harsh techniques abhorred by the CITF, and the CIA went even further. It was responsible for one of the most notorious cases at Guantánamo, the waterboarding of the self-confessed al-Qaida leader Khalid Sheikh Mohammed. The CIA had relative independence. It ran a secret camp, Camp Seven, whose existence only became public late in 2008.

Also operating on the island was the FBI, which approached interrogations in much the same way as the CITF and opposed waterboarding and similar methods. Jane Mayer, in her book The Dark Side, records one interrogation in which the FBI claimed to have been getting "phenomenal" information, only to be pushed out by a CIA team. The FBI, fearful of being implicated in something potentially illegal, fled the scene.

The role of psychologists and psychiatrists has raised medical ethical questions, given that some participated in interrogations. One of the files shows a behavioural science team winning a rare victory over the JTF GTMO in December 2003. The behavioural team assessed a detainee as "high threat" while the JTF GTMO had him as "medium threat". JTF GTMO deferred to the behavioural team.

As if the mix was not volatile enough, also on the island base at various times were intelligence officers from other countries. One of the files records that "from 3 to 10 August 2002 Pakistani intelligence officers interrogated" a detainee. Adding to the confusion, another file claims that another detainee, described by JTF GTMO as a "high risk", was also a Pakistani intelligence agent.

The early JTF GTMO commanders included Major General Michael Dunlavey and Major General Geoffrey Miller, whose names appear at the bottom of many of the detainee reports. They came under a lot of pressure from Washington to produce results after a first year that yielded little intelligence.

Miller is controversial, having served at Guantánamo from November 2002 to August 2003 before being transferred to run prisons in Iraq.

He has been accused of introducing tactics used at Guantánamo to Iraq, blurring the line between guard duties and interrogation, a move that could have contributed to the Abu Ghraib scandal.

The chain of command from Guantánamo to Washington is illustrated by a request sent by Miller's predecessor Dunlavey in 2002 which, according to a Senate investigation, asked for authorisation to use harsher interrogation techniques.

It went first to General James Hill, the commander of US Southern Command, the recipient of the detainee reports. Hill forwarded it to General Richard Myers, who was chairman of the joint chiefs of staff. The chairman of the joint chiefs is the highest-ranking military officer in the US and advises both the president and defence secretary.

There was some resistance to such requests in Washington, from figures such as Powell and, to a lesser extent, Rice. But the dominant mood was in favour of harsh methods. Cheney is unrepentant: in a rare public foray he made a speech in 2008 in Washington denying that waterboarding constituted torture and insisting that the information obtained from interrogations saved lives. That line is repeated by Rumsfeld in his autobiography published this year, and Bush in his in November.

"No doubt the procedure was tough but medical experts assured the CIA that it did no lasting harm," Bush wrote.