He is 54 but looks 70 – "like an Indian yogi with a long white beard," as ex-Colonel Mohamed el-Ghanem's Swiss lawyer puts it. "I entered his cell – I had a Swiss official next to me who formally introduced me. Colonel Ghanem was sitting on his bed with his feet on the floor. Then he lay on the bed and pulled the blanket up to his chin. He did not say a word – not a single word. For much of the time, he shut his eyes."

Pierre Bayenet specialises in human rights cases but admits that ex-President Mubarak's former Interior Ministry colonel – locked up for six years without trial in a Swiss prison after accusing the Swiss security services of blackmailing him – is one of the strangest cases he has even been involved in. As a journalist, I must say the same. I met Colonel Ghanem in Cairo 12 years ago, a tough, English-speaking military man who opposed Mubarak for his bias against Egypt's Christian Copts, the Egyptian government's corruption, nepotism, torture and human rights abuses. His interview with me provoked a blaze of harassment from the Egyptian security police, until he was given temporary political asylum in Switzerland.

In any other world, he would now be a hero of the Egyptian revolution, one of the first police officers to revolt against the dictator overthrown a year ago. Instead, he has been fingered by the Swiss security service as a dangerous Islamist subversive, slandered by a Swiss police officer for a Geneva assault which never took place, prevented from meeting his sister-in-law after Swiss security talked to the FBI, and now sits – refusing to talk even to his own lawyer – in a Geneva prison cell.

"He has lots of papers in his cell which appear to have been written by him about his case," Mr Bayenet says. "He lay there with his eyes shut. I told him about his brother Ali's attempt to see him, I said that I was meeting you, Robert. These were the only times he reacted. He opened his eyes and closed them again. He was listening to every word. I told him Ali thought he might be dead. I told him you were following his case. I was in the end rather positive – at least he didn't tell me to go!" Doctors at the prison told Mr Ghanem about the Egyptian revolution. He did not respond.

When I met Colonel Ghanem in the garden coffee shop of the Cairo Marriott Gezira hotel in 2000, he was well-shaven, fit, bespectacled and passionate, a trifle on the plump side but looking no more than his 42 years, raging against Mubarak's refusal to permit Christians in Egypt to build more churches. He held a PhD in law from Rome University, was the author of a 1991 book on "the law and terrorism", an unlikely whistleblower – but he desperately appealed to me to seek Amnesty's help. When he tried to leave his country, members of his own police force turned him back at Cairo airport.

A year later, Colonel Ghanem called me in Beirut from Geneva to say that the Swiss had granted him temporary asylum. He was going back to study at university. But when he called me again in 2003, something had gone dreadfully wrong. The Swiss secret police, he told me, were trying to force him to penetrate local al-Qa'ida cells and Switzerland's Arab community. He had refused to co-operate, he said, and now they were threatening him.

I thought no more of this weird claim until, in 2008, his brother Ali, who lives in Washington, contacted me. He had been refused permission to see Mohamed el-Ghanem, who since 2007 had been imprisoned without trial – and had been told by the Swiss authorities that Mohamed "did not want to see him". Ali feared that his brother was dead.

According to Ali, the Swiss had reacted after Mr Ghanem had allegedly written an internet article which turned up on Islamist websites, claiming that Switzerland was "the most contemptible among the enemies of Islam," since it supported the 2003 American invasion of Iraq, stood behind Mubarak's "renegade regime" and was now trying "to penetrate Muslim society to collect intelligence". When the UN's "Enforced and Voluntary Disappearances" experts asked why Mr Ghanem had been locked up, the authorities told them – in the English version of the report – that it was because of his "dangerousness". Even the French expression they used – "dangerosité" – was very odd. How, I asked myself, could an anti-Mubarak cop who defended Christians, have written such poisonous remarks about his country of asylum. If indeed he wrote them.

For there is clear evidence that the Swiss secret service – not exactly renowned among the world's state-of-the-art intelligence outfits – has been deeply involved in Mr Ghanem's case and has indeed been seeking to penetrate Muslim groups in Switzerland. In January 2005, for example, Mr Ghanem complained that he had been requested to spy on Hani Ramadan, an Egyptian member of the Muslim Brotherhood – now dominating the new Egyptian parliament – who ran an Islamic Centre in Geneva.

Mr Ghanem says he refused. Only two years later did the Swiss parliament investigate an official intelligence operation – "Operation Memphis" – organised against Mr Ramadan and using informants to seek information about Mr Ramadan's contacts. Mr Ghanem is not mentioned in this report – but it strongly suggests that he was telling the truth. There followed a long series of legal applications and arguments over Mr Ghanem's mental health, his claim of habeas corpus and – of course – his "dangerousness". This revolved around three incidents in which Mr Ghanem claimed he was under observation.

In July 2004, three years after he arrived in Switzerland, he filed a complaint about a man who supposedly "bumped into him" in a Geneva street, a black African who allegedly broke his glasses. Just over a year later, he complained to the police that his phone was tapped and that he was being followed by Egyptian government agents.

Then in February 2005, Mr Ghanem was accused of assaulting a Somali on the campus of Geneva university. According to Mr Ghanem, the man was aggressive and he confronted him with a bread knife. The man supposedly hit Mohamed. After several months of incarceration, Mr Ghanem was released.

But then the Swiss security services stepped in. Mr Urs von Daeniken of the Federal Police "service d'analyse et de prévention", the Swiss intelligence service, wrote on 6 October 2005 to the judge who had heard Mr Ghanem's case, quoting from the internet article supposedly written by Mr Ghanem. The letter – a copy of which is in the possession of The Independent – claimed that Mr Ghanem had also threatened leading Swiss personalities with unspecified "consequences". He was a "violent" man who was threatening the "internal and external security of Switzerland".

Mr Ghanem insists that although he was prepared to defend himself against his alleged assailant in February, 2005, he never attacked the man with his knife. The alleged victim also says that he was never touched by Mr Ghanem, although he says the Egyptian was holding a knife. But then on 25 October, just 19 days after Mr Von Daeniken's letter, a Geneva police officer wrote to the judge to say that Mr Ghanem had "seriously wounded" an African at Geneva university and had "stabbed him with a kitchen knife in the abdomen".

The police officer – whose name is known to The Independent – was "obviously lying", according to lawyer Pierre Bayenet, since even the alleged victim said that he had not been touched by the accused.

The police officer's letter repeated the internet quotations, adding that these were "alarmist and hateful, repeated over a period of several months... and provoked the kind of reactions you can imagine". The letter made no reference to what these "reactions" were. In any event, Mr Ghanem – who all along had alleged that the Swiss security authorities were trying to coerce him to spy on his fellow Muslims – had now attracted the public interest of the very secret service and police force who were now writing letters to a trial judge.

Colonel Ghanem has undergone psychiatric examination; his lawyer believes he almost died before Christmas. Mr Bayenet also says that – having failed to recruit Mr Ghanem and having then harassed him and made a false claim of assault against him – the Swiss authorities would now like to deport the Egyptian. "But after their claims against him, who would give him asylum now?" Mr Bayenet asks. "Would he be safe in Egypt? Could they send him back there?"