While the Foreign Office denied the claims, the mercenaries insisted Mr Cook had issued a licence which allowed them to break UN sanctions and ship arms to Sierra Leone.
Yesterday it was revealed an investigation into the allegations has been launched by the National Investigation Service (NIS), an arm of Customs and Excise.
In an unprecedented step, it will this week question Peter Penfold, the High Commissioner for Sierra Leone, into claims that he colluded with the mercenaries and may even have asked for their assistance.
The claims, that last night threatened to become increasingly embarrassing for a government which has made great play of its ethical foreign policy, focus on Sierra Leone, the former British colony in West Africa. In May last year, the elected President Ahmad Tejan Kabbah, was ousted in a coup led by Johnny Paul Koroma.
Mr Tejan was restored to power in March with the assistance of the British- based "military consultants" Sandline International, headed by Lieutenant- Colonel Tim Spicer, the army's spokesman in Bosnia.
The Customs investigation will centre on the shipment by Sandline of 30 tonnes of weapons and ammunition to President Kabbah's supporters. Officers will decide whether the shipment, from Bulgaria, breached United Nations sanctions imposed last November.
But last night Sandline claimed it had acted with the approval of the Government. In a statement Lt-Col Spicer said that he "understood and still believed that we were acting with the approval of Her Majesty's Government in assisting to restore President Kabbah."
He added: "President Kabbah's government has at all times remained the only internationally recognised lawful government of Sierra Leone."
A spokeswoman for Sandline said last night that the company had a licence from the Foreign Secretary permitting it to ship the weapons, and in effect break the sanctions.
The weapons and training that Sandline provided to the Kabbah-supporting militia and the Nigerian army, which also supported the former president, may have been crucial to the success of the counter coup. The weapons were flown out of Sofia, Bulgaria, on or around 21 February. Mr Kabbah - who attended the Commonwealth summit in Edinburgh last year while still in exile - was restored to power in March.
The NIS officers will question Mr Penfold, a career diplomat and former Governor of the British Virgin Islands, about his links with Sandline. Following Mr Kabbah's return to power, the Government admitted that Mr Penfold had spoken to the company but refused to reveal the details of the conversations.
It is understood the talks took place in Conakry, Guinea, where Mr Kabbah had been exiled. The British diplomatic mission in Sierra Leone also transferred to Guinea from Freetown following the Koroma takeover.
"Central to the inquiry will be whether Mr Penfold knew about the arms supply and whether he was involved," a Customs source said last night.
Last night the Foreign Office said it had asked Customs to investigate the matter and had also launched its own inquiry.
"In the meantime the Foreign Office can confirm that no ministerial approval was ever given for Sandline's activities," said a spokeswoman. She added that Mr Penfold, who is now back in Britain, was "co-operating fully" with Customs.
Shadow Trade and Industry secretary John Redwood last night demanded the Government make it clear whether there had been any collusion.
"I want Robin Cook to come before the Commons and say what has been happening," he said. "We need to get to the bottom of this and Mr Cook has to come clean."
Last night at Westminster there were fears that Mr Penfold may be used as a scapegoat.
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