Omar Sheikh, a British-born Islamist militant, is waiting to be hanged in Pakistan for a murder he almost certainly didn't commit - of the Wall Street Journal reporter Daniel Pearl in 2002. Both the US government and Pearl's wife have since acknowledged that Sheikh was not responsible. Yet the Pakistani government is refusing to try other suspects newly implicated in Pearl's kidnap and murder for fear the evidence they produce in court might acquit Sheikh and reveal too much.

Significantly, Sheikh is also the man who, on the instructions of General Mahmoud Ahmed, the then head of Pakistan's Inter-Services Intelligence (ISI), wired $100,000 before the 9/11 attacks to Mohammed Atta, the lead hijacker. It is extraordinary that neither Ahmed nor Sheikh have been charged and brought to trial on this count. Why not?

Ahmed, the paymaster for the hijackers, was actually in Washington on 9/11, and had a series of pre-9/11 top-level meetings in the White House, the Pentagon, the national security council, and with George Tenet, then head of the CIA, and Marc Grossman, the under-secretary of state for political affairs. When Ahmed was exposed by the Wall Street Journal as having sent the money to the hijackers, he was forced to "retire" by President Pervez Musharraf. Why hasn't the US demanded that he be questioned and tried in court?

Another person who must know a great deal about what led up to 9/11 is Khalid Sheikh Mohammed, allegedly arrested in Rawalpindi on March 1 2003. A joint Senate-House intelligence select committee inquiry in July 2003 stated: "KSM appears to be one of Bin Laden's most trusted lieutenants and was active in recruiting people to travel outside Afghanistan, including to the US, on behalf of Bin Laden." According to the report, the clear implication was that they would be engaged in planning terrorist-related activities.

The report was sent from the CIA to the FBI, but neither agency apparently recognised the significance of a Bin Laden lieutenant sending terrorists to the US and asking them to establish contacts with colleagues already there. Yet the New York Times has since noted that "American officials said that KSM, once al-Qaida's top operational commander, personally executed Daniel Pearl ... but he was unlikely to be accused of the crime in an American criminal court because of the risk of divulging classified information". Indeed, he may never be brought to trial.

A fourth witness is Sibel Edmonds. She is a 33-year-old Turkish-American former FBI translator of intelligence, fluent in Farsi, the language spoken mainly in Iran and Afghanistan, who had top-secret security clearance. She tried to blow the whistle on the cover-up of intelligence that names some of the culprits who orchestrated the 9/11 attacks, but is now under two gagging orders that forbid her from testifying in court or mentioning the names of the people or the countries involved. She has been quoted as saying: "My translations of the 9/11 intercepts included [terrorist] money laundering, detailed and date-specific information ... if they were to do real investigations, we would see several significant high-level criminal prosecutions in this country [the US] ... and believe me, they will do everything to cover this up".

Furthermore, the trial in the US of Zacharias Moussaoui (allegedly the 20th hijacker) is in danger of collapse apparently because of "the CIA's reluctance to allow key lieutenants of Osama bin Laden to testify at the trial". Two of the alleged conspirators have already been set free in Germany for the same reason.

The FBI, illegally, continues to refuse the to release of their agent Robert Wright's 500-page manuscript Fatal Betrayals of the Intelligence Mission, and has even refused to turn the manuscript over to Senator Shelby, vice-chairman of the joint intelligence committee charged with investigating America's 9/11 intelligence failures. And the US government still refuses to declassify 28 secret pages of a recent report on 9/11.

It has been rumoured that Pearl was especially interested in any role played by the US in training or backing the ISI. Daniel Ellsberg, the former US defence department whistleblower who has accompanied Edmonds in court, has stated: "It seems to me quite plausible that Pakistan was quite involved in this ... To say Pakistan is, to me, to say CIA because ... it's hard to say that the ISI knew something that the CIA had no knowledge of." Ahmed's close relations with the CIA would seem to confirm this. For years the CIA used the ISI as a conduit to pump billions of dollars into militant Islamist groups in Afghanistan, both before and after the Soviet invasion of 1979.

W ith CIA backing, the ISI has developed, since the early 1980s, into a parallel structure, a state within a state, with staff and informers estimated by some at 150,000. It wields enormous power over all aspects of government. The case of Ahmed confirms that parts of the ISI directly supported and financed al-Qaida, and it has long been established that the ISI has acted as go-between in intelligence operations on behalf of the CIA.

Senator Bob Graham, chairman of the Senate select committee on intelligence, has said: "I think there is very compelling evidence that at least some of the terrorists were assisted, not just in financing ... by a sovereign foreign government." In that context, Horst Ehmke, former coordinator of the West German secret services, observed: "Terrorists could not have carried out such an operation with four hijacked planes without the support of a secret service."

That might give meaning to the reaction on 9/11 of Richard Clarke, the White House counter-terrorism chief, when he saw the passenger lists later on the day itself: "I was stunned ... that there were al-Qaida operatives on board using names that the FBI knew were al-Qaida." It was just that, as Dale Watson, head of counter-terrorism at the FBI told him, the "CIA forgot to tell us about them".

· Michael Meacher is Labour MP for Oldham West and Royton. He was environment minister 1997-2003

massonm@parliament.uk