The Ministry of Defence says an investigation will be launched into claims that an inquiry it set up to examine whether British troops abused Iraqi prisoners has become "little more than a whitewash".

Louise Thomas, an official working with the inquiry team who says she has resigned in protest at the lack of progress, spent six months working with the Iraq Historic Allegations Team (IHAT), which was set up in response to a growing number of complaints from former prisoners. Many were detained at a secretive interrogation centre that the British military operated in the south-east of the country.

Thomas, 45, a former Wren who also served as a police officer for five years, told the Guardian she had seen around 1,600 videos of interrogation sessions, a number of which showed prisoners being abused, humiliated and threatened.

They suggested that some of the detainees were being subject to extreme sleep deprivation and beaten between interrogation sessions.

Thomas alleges that the abuses recorded in the videos are being investigated in an ineffective manner, by investigators who sometimes show little concern for what they are seeing, and that not all relevant material has been handed over to the inquiry by the MoD.

"I saw a really dark side of the British army," Thomas said. "The videos showed really quite terrible abuses. But some of the IHAT investigators just weren't interested."

The MoD said any allegations of inappropriate conduct or inattention to duty by IHAT members would be investigated by IHAT's management and that appropriate action would be taken.

A Ministry of Defence spokesman said: "All of these allegations of abuse are known to the Ministry of Defence and Iraq Historical Allegations Team (IHAT) which is why the independent IHAT is already investigating them.

"The MoD has cooperated fully, including the provision of all known evidence.

"We are confident in the IHAT's abilities and following the outcome of their investigations, action will be considered against individuals where appropriate. Any criticisms about IHAT itself are for the organisation to answer."

The abuse allegations focus on a joint services interrogation centre under Intelligence Corps command, the Joint Forces Interrogation Team (JFIT), that operated at three locations in the Basra area between March 2003 and December 2008.

In November 2010, JFIT was described in the high court by lawyers representing the prisoners as "Britain's Abu Ghraib".

Thomas alleges that some IHAT investigators, based at the inquiry's headquarters on a military base near Pewsey, in Wiltshire, show little interest in the contents of the videos, making comments such as "who cares, they're terrorists?" or "they're only bombers".

"They would laugh at me, because I was interested and concerned. They would say 'Here comes Miss Marple' when I came by."

She added that she was concerned that IHAT was "little more than a whitewash", rather than a genuine investigation.

Thomas said that on the day she resigned from IHAT she lodged a three-page document in which she raised serious concerns about the way in which the contents of the videos were being investigated, and added that she had made a number of previous written complaints.

Thomas is known to have given a witness statement to lawyers representing the former prisoners, in which she raises her concerns about IHAT.

During her time working at IHAT, Thomas says she discovered that custody records prepared at JFIT at the same time as the videos suggest that not all the interrogation videos that were recorded have been disclosed to IHAT. She also alleged that IHAT investigators have on occasion had difficulty accessing data held on an MoD computer. In her interview with the Guardian, Thomas alleged that the videos of interrogations showed:

• Prisoners threatened with rape during interrogation.

• Prisoners being told they were to be hanged and given a detailed description of the mechanics of hanging.

• An adolescent boy being interrogated and his father being allowed briefly into the room to hug him.

• A man being interrogated while naked from the waist down.

• One prisoner having acquired a black eye in between interrogation sessions.

• Prisoners complaining of starvation.

• A prisoner aged around 50 begging for a hours to be allowed to relieve himself.

• Young guards holding exhausted prisoners upright while an interrogator screams at them: "Hold the fucker up!"

• Frequent use of "harshing", which entails several interrogators screaming at a single prisoner from a distance of a few inches.

Thomas also alleged that military witnesses have given statements to IHAT saying that detainees at JFIT were handed over to US forces after being told that they were to be hanged, and that the US troops who took them into detention made hanging motions to the prisoners, with their hands around their own throats.

Her description of the contents of the videos corroborates descriptions previously given to the Guardian by a senior investigator with a detailed knowledge of the IHAT inquiry. A former soldier who served as a guard at JFIT has confirmed that he and others were ordered to take hold of blindfolded prisoners by their thumbs in between interrogation sessions, then drag them around assault courses, where they could not be filmed.

He also confirmed that the prisoners were often beaten during these runs, and that they would then be returned for interrogation in front of a video camera.

This is an allegation that has already been made by many of the 149 former prisoners who have come forward to lodge complaints.

This individual also said that soldiers serving as guards would be ordered to take hold of prisoners who were unable to stand as a result of sleep deprivation and keep them upright during interrogation, something that Thomas says is recorded in one of the videos she has seen.

A small number of videos depicting interrogations have been made public and have appeared on the Guardian's website. One shows an exhausted prisoner being threatened with death, intimidated, subjected to sensory deprivation and complaining of starvation before being ordered to place blackened goggles over his eyes and led away by his thumbs.

Another shows an interrogator telling a prisoner who complains of being in pain: "Good, I'm fucking glad. I hope you die. I hope your kids die."

This prisoner too is led away by his thumbs while blind-folded, for what the interrogator calls "a quick run".

The MoD has accepted that the men may have been tortured, with the high court stating in a judgment in December 2010 that "it is accepted on behalf of the secretary of state [for defence] that the individual allegations raise an arguable case of breach of article 3" – the article of the European Convention on Human Rights that protects individuals from torture or cruel treatment.

The MoD insists that IHAT complies fully with the British government's obligations under the convention to establish an investigation that is both effective and independent.

Lawyers for the former prisoners have said repeatedly that IHAT lacks sufficient independence, as too many members of the Royal Military Police have been involved with it in the past; that it lacks rigour, with no charges having been brought two years after it was established; and is insufficiently independent of the MoD, as it answers to senior officials at the ministry.

Last November, after learning that RMP officers were involved with IHAT, the appeal court said "it is impossible to avoid the conclusion that IHAT lacks the requisite independence". This led to RMP officers being replaced – although Thomas says that this did not happen immediately.

The former prisoners' lawyers say there needs to be a public inquiry into the army's detention and interrogation practices in the south-east of Iraq.

The MoD has said that "a costly new public inquiry is not necessary or appropriate", and that IHAT is better able to investigate individual criminal behaviour in a way that would serve the interests of justice.

A senior source with knowledge of the IHAT investigation said that he believed any failure to disclose interrogation videos would have been the result of error rather than concealment.

He added that he hoped it was not correct that some IHAT staff were dismissive of the contents of the videos, believing that senior members were committed to their task.

He conceded, however, that "there could be an element of upstairs, downstairs" that limited senior managers' awareness of how more junior investigators were conducting themselves.

MoD response to mounting allegations

The Iraq Historic Allegations Team (Ihat) was set up by the Ministry of Defence in 2010 as a result of a growing number of claims of abuse of Iraqi civilians by British troops.

Allegations were made against the troops in the wake of the killing of Baha Mousa, an Basra Iraqi hotel worker who died in 2003 while in British custody, and the Battle of Danny Boy in 2004 where it is alleged that British soldiers tortured and murdered Iraqi gunmen after a firefight. Many of the allegations refer to interrogations by British troops at the Shaibah detention centre in Basra.

"The establishment of the Ihat should not be taken as an admission of fault or failure," Nick Harvey, then armed forces minister, said when the unit was set up. He added: "These allegations are as yet unproven, but their existence is corrosive to both the morale and reputation of our armed forces. We owe it to them, and the complainants, to properly investigate these allegations and that is exactly what the Ihat have now started to do."

One soldier, a corporal, was jailed over Mousa's death and a further 19 are to be investigated. Three of those have been suspended from duty.

The allegations behind the Battle of Danny Boy, now being investigated by the al-Sweady inquiry, include murder. They have been denied by the army and Ministry of Defence. The al-Sweady inquiry has so far identified more than 500 troops who will have to give evidence and who will also be interviewed, beforehand, by Ihat. Members of the SAS, the SBS, and interrogators from a unit called the Joint Support Group are also likely to be questioned.

Ihat is reported to have now identified more than 100 serving and former members of the armed forces who they want to interview relating to the alleged torture and abuse of Iraqi civilians. That number is expected to increase significantly.

The team has been led by a retired senior civilian policeman and now includes navy police and ex-civilian police detectives. Army police and provosts (military personnel responsible for security and detention) were excluded last November after the appeal court said it was "impossible to avoid the conclusion that IHAT lacks the requisite independence". The court added: "The problem is that the Provost Branch members of IHAT are participants in investigating allegations which, if true, occurred at a time when Provost Branch members were plainly involved in matters surrounding the detention and internment of suspected persons in Iraq … We are of the view that the practical independence of IHAT is, at least as a matter of reasonable perception, substantially compromised".

In an al-Sweady hearing this summer, Jonathan Acton Davis QC, counsel to the inquiry, said IHAT had purchased a newly designed forensic computer system called the Forensic Data Handling Capability (FDHC). Once fully built, it could hold in the region of 110 terabytes of data and was "likely to be the largest storage computer currently in operation in the United Kingdom", Acton Davis said.

He said that IHAT staff had cooperated well with the al-Sweady inquiry but added that "a series of technical and logistical issues have blighted that co-operation".

IHAT said it was collecting information from the defence and security centre at Chicksands in Befordshire, the Permanent Joint Headquarters at Northwood, north-west London, and data "forensically recovered from the MoD's "corporate memory". Richard Norton-Taylor