The Foreign Secretary - who sought to deflect criticism by announcing an extra pounds 10m in aid for the war-torn region - was accused of failing to answer a number of "serious charges" against his department and in particular those against one of his ministers, Tony Lloyd.
The aid package, to be paid from the Foreign Office's own reserve, will boost the Nigerian-led Ecomog force, which is trying to restore President Kabbah to full power.
But during a Tory-led debate, Michael Howard, the shadow foreign secretary, said that the inquiry reports of Sir Thomas Legg and the Foreign Affairs Select Committee had both blamed ministers for "deliberately mis-stating the scope and the nature of the arms embargo to Sierra Leone".
He went on: "This was especially serious as the Government made an Order in Council implementing the embargo, which created a criminal offence with a maximum penalty of seven years' imprisonment."
Any role the Foreign Secretary played in the leaking of the hard-hitting Foreign Affairs Select Committee's report by the Labour MP Ernie Ross (Dundee W) is already being investigated by the Commons Standards and Privileges Committee. The report dealt with the breach of an arms embargo by Sandline, a British firm.
But Mr Cook, who was forced to delay a trip to Russia because of the debate, said the real issue was the continuing suffering of the people of Sierra Leone.
"Sandline's role has been absolutely irrelevant to the military activities on the ground and absolutely irrelevant to most of the people of Sierra Leone," he insisted.
Mr Cook said Britain had done more than any other Western power to help the people of Sierra Leone through diplomatic support and aid and the extra pounds 10m would provide further support for Ecomog, help to train a "democratically accountable" military force, encourage the rebels to give up their weapons and promote demilitarisation.
Launching his defence, Mr Cook stressed he would accept any recommendations of the select committee's report and would announce any changes to arms embargoes to Parliament.
"I agree that all officials should be doubly careful in contacts with persons under criminal investigation and I have instructed them to consult first with our legal advisers.
"I agree with them on the need for action against arms brokering, and the Government is currently considering the responses to its proposals on its recent White Paper on the subject.
"I believe that the committee is right to be concerned about the particular sensitivities in dealing with military companies whose staff include former members of the armed forces or intelligence agencies.
"And I share their view that Colonel Spicer (chief of Sandline) should have known more about the legal position of the supply of arms and was less than frank with Foreign Office officials about the supply of arms."
The committee's report had found that there had been an "appalling" failure by the Foreign Office in its handling of the affair.
But Mr Cook told MPs: "Their report does not raise the slightest doubt about the central findings of Legg inquiry - that there was no connivance in the Foreign Office of a breach of the arms embargo and there was no conspiracy by either officials or ministers to undermine the publicly stated policy."Reuse content