The CIA has videotapes of September 11, 2001 plotter Ramzi Binalshibh being interrogated in a secret overseas prison.

Discovered under a desk, the recordings could provide an unparalleled look at how foreign governments aided the United States in holding and questioning suspected terrorists. The two videotapes and one audiotape are believed to be the only remaining recordings made within the clandestine prison system.

The tapes depict Binalshibh’s interrogation sessions at a Moroccan-run facility the CIA used near Rabat in 2002, say several current and former US officials. They spoke on condition of anonymity because the videos remain a closely guarded secret.

When the CIA destroyed its cache of 92 videos of two other al Qaeda operatives, Abu Zubaydah and Abd al-Nashiri, being waterboarded in 2005, officials believed they had wiped away all of the agency’s interrogation footage. But in 2007, a staffer found a box tucked under a desk in the CIA’s Counterterrorism Centre and pulled out the Binalshibh tapes.

A Justice Department prosecutor who is already investigating whether destroying the Zubaydah and al-Nashiri tapes was illegal is now also probing why the Binalshibh tapes were never disclosed. Twice, the Government told a federal judge they did not exist.

The tapes could complicate US efforts to prosecute Binalshibh, 38, who has been described as a “key facilitator” in the September 11, 2001, attacks.

If the tapes surfaced at trial, they could clearly reveal Morocco’s role in the Greystone counterterrorism programme, which authorised the CIA to hold terrorists in secret prisons and shuttle them to other countries.

More significantly to his defence, the tapes also could provide evidence of Binalshibh’s mental state within the first months of his capture.

In court documents, defence lawyers have been asking for medical records to see whether his years in CIA custody made him mentally unstable. He is being treated for schizophrenia with a potent cocktail of anti-psychotic medications.

With military commissions on hold while the Obama Administration figures out what to do with suspected terrorists, Binalshibh has never had a hearing on whether he is mentally fit to stand trial.

The CIA first publicly hinted at the existence of the Binalshibh tapes in 2007 in a letter to US District Judge Leonie Brinkema in Virginia. The Government twice denied having such tapes, and recanted once they were discovered. But the Government blacked out Binalshibh’s name from a public copy of the letter.

At the time, the CIA played down the significance, saying the videos were not taken as part of the CIA’s detention programme and did not show CIA interrogations. That’s true, but only because of the unusual nature of the Moroccan prison, which was largely financed by the CIA but run by Moroccans, the former officials said.

The CIA could move detainees in and out, and oversee the interrogations, but officially, Morocco had control.

Moroccan Government officials did not respond to questions about Binalshibh and his time in Morocco. The country has never acknowledged the existence of the detention centre.

But current and former US officials say no harsh interrogation methods, such as waterboarding, were used in Morocco. In the CIA’s secret network of undisclosed “black prisons”, Morocco was a place to hold detainees for a few months at a time.

“The tapes record a guy sitting in a room just answering questions,” according to a US official familiar with the programme.

That would make them quite different from the 92 interrogation videos of Zubaydah and al-Nashiri being subjected to waterboarding and other harsh interrogation tactics.

Binalshibh was captured on September 11, 2002, and interrogated for days at a CIA facility in Afghanistan. Almost immediately, two former CIA officials said, Binalshibh exhibited mental instability that would worsen over time.

Though Binalshibh was unco-operative during his early interrogations, his interviews formed the foundation for parts of the September 11 commission report.

One official said he also provided intelligence about a plot to crash aircraft into London’s Heathrow Airport.

Binalshibh spent five months in Morocco in late 2002 and early 2003, the first of three trips through the facility during his years in CIA custody.

Since his incarceration was established at Guantanamo Bay in 2006, Binalshibh has appeared increasingly erratic.

Court records show him acting out, breaking cameras in his cell and smearing them with faeces.

He has experienced delusions, believing the CIA was intentionally shaking his bed and cell, according to court records and interviews. He has imagined tingling sensations as if things were crawling all over him and developed a nervous tic, obsessively scratching himself.

Nine years after his capture, there is no indication when Binalshibh will face a military or civilian trial.