In a planted Parliamentary answer last night Mr Cook made the damaging admission that five intelligence reports seen by officials at the Foreign Office linked Sandline with the supply of arms or military equipment to Sierra Leone.
Last night both main opposition parties demanded that the Foreign Secretary should come to the House of Commons in person to explain himself.
Only last Tuesday, Mr Cook had assured MPs: "At no stage over the past months was any intelligence passed to ministers or officials that suggested a breach of the arms embargo."
The disclosure shows just how much information was withheld from ministers by senior officials over the affair and also underlines just how deeply involved and well-briefed MI6 was about it. But it will also be politically embarrassing for Mr Cook.
The Independent understands that the five reports were sent to the Foreign Office after the beginning of February. It is likely they were seen by officials on the equatorial-Africa desk.
The confirmation that MI6 knew about Sandline's activities does raise questions about how the service handled the information and why it was apparently missing from the intelligence digests it prepares for ministers.
Last Thursday the Permanent Secretary of the Foreign and Commonwealth Office, Sir John Kerr, told MPs that he knew six weeks ago of allegations that his staff colluded in the shipment of arms to the exiled President Kabbah. He did not tell the Foreign Secretary, he added, because it was a "housekeeping matter" and Mr Cook was busy. Mr Cook only found out at the end of April when he received a letter from Sandline's solicitors.
Officials said last night that the Foreign Secretary had taken the first possible opportunity to correct the misleading impression that he had inadvertently given.
In his reply to Charles Clarke, Labour MP for Norwich South, he said Sir Thomas Legg's independent inquiry into the affair would have access to intelligence reports as well as to all other official documents referring to Sandline. The newly discovered reports were written and delivered between 8 October last year - when the UN passed a resolution banning arms to Sierra Leone - and 10 March this year, when a Customs & Excise investigation began.
"We are aware of five intelligence reports ... which refer to Sandline, or companies associated with Sandline, and to the supply of arms or military equipment. They were seen by officials but not by ministers," Mr Cook's reply said.
Michael Howard, Shadow Foreign Secretary, said the answer clearly showed that Mr Cook had misled MPs. "He should therefore come to the House and apologise at the earliest opportunity," he said.
Menzies Campbell, the Liberal Democrat foreign affairs spokesman, said the mistake should be rectified immediately.
"This written answer only serves to add to the confusion and speculation of the last two weeks. Mr Cook will almost certainly have to come to the House of Commons to explain this apparent discrepancy," he said.
It seems Mr Cook only found out about the intelligence reports after he answered a Conservative-sponsored debate on the issue on Monday. Mr Clarke's question was put down on Monday evening for answer yesterday.
The official code of conduct for ministers says it is of "paramount importance" that they give accurate and truthful information to Parliament and that they correct any error at the earliest opportunity.
However, there is no reason to suspect that Mr Cook knowingly misled the House - a clear resigning matter.Reuse content