The disclosure of a ministerial split undermined the attempts by Downing Street to smooth over the secret deal between Tony Blair and US President Bill Clinton for Britain to take the shipment to avert the risk of it falling into wrong hands.
The President of the Board of Trade and the "green" minister at the Department of Trade and Industry, John Battle, blocked on "at least a dozen occasions" plans to ship enriched uranium for reprocessing, it was confirmed by Whitehall sources.
"Margaret and John took a very principled stand on this one. We were fed up with the Foreign Office saying: "We are the ones with an ethical foreign policy and the DTI is unethical," one senior source said.
The disclosure that the two ministers refused to sanction the shipment - which took place without incident seven days ago - is likely to strengthen protests in Scotland over the decision to accept shipments from the former Soviet republic.
It emerged yesterday that the deal came close to collapse. Senior DTI figures were angry at what they saw as both an attempt to pass the buck and "ethical posturing" by the Foreign Office.
After being first raised in late summer, the proposal was not agreed by DTI ministers until shortly before the turn of the year.
The ministers eventually agreed to sign the licence only on condition that the Foreign Office would take any political flak from the announcement.
Questions about the shipment, when news leaked in Washington, were handled last week by the Foreign Office, and the Foreign Office minister, Doug Henderson, dealt with an emergency statement in the House.
The trade ministers also signed because they were fearful that a separate deal they were brokering to bail out British coal mines might not win full cabinet backing if they dug in over the nuclear issue.
But the ministers were unhappy at being pressurised by Mr Cook and his officials to overturn its principle that no nuclear material would be reprocessed unless it was later returned to its country of origin.
Downing Street continued to insist yesterday that it was agreed through the "appropriate cabinet committee in the usual way".
Mr Battle said: "Questions have always to be asked as policy is prepared but there is no doubt that accepting this fuel contributes to international nuclear non-proliferation. I think this was the right decision.
"I am absolutely convinced it is in safe hands at Dounreay. It is much safer there than anywhere else in the world."
A senior Foreign Office spokesman said: "It was the Government's decision to do what we did.
"It was a government decision in which the Prime Minister was closely involved and which followed consultations with the Americans and other partners over a long period.
"It really is not helpful or accurate to portray this in terms of a division between two government departments. This is a government decision."Reuse content