Ministers have insisted that their purchase was based on expert advice within the Department of Health with outside assistance, including the Ministry of Defence.

But national security considerations have prevented the health secretary, Alan Milburn, being able to justify the decision scientifically in the face of claims that the contract to provide 20 million jabs went to Powderject because its boss, Dr Paul Drayson, gave £100,000 to the Labour party.

With the Bush administration purchasing 200 million doses of the rival EM63 vaccine, developed by the Soviet Union in the 1950s in its narrowly-successful effort to avoid a smallpox epidemic being spread by a traveller from India, the pressure to explain Whitehall's decision intensified yesterday.

Steve Prior, a senior scientist at the reputable Potomac Institute in Washington, told the Times that trials in the US had suggested that the EM63 vaccine stands up to the most likely threat - a smallpox virus developed from the Indian strain and known as the "battle strain" - better than the Lister vaccine in the kind of epidemic conditions which homeland defence planners believe the west faces from states like Iraq.

As the most feared possible assailant, Iraq is assumed to have the battle strain virus from old Soviet stockpiles. It was the only source left outside the US after smallpox was officially eradicated in 1980. The Lister strain, Dr Prior claimed, is better at protecting populations where smallpox has already been wiped out. The point is disputed.

The World Health Organisation and independent scientists told the Guardian earlier this year that the different vaccines were equally effective in countering different strains of smallpox. Department of Health sources stressed last night, as they did throughout the controversy over the £28m Powderject contract - and Dr Drayson's two £50,000 donations - that they acted on scientific and military advice. "Our problem is that we cannot really talk about our reasons."

But Dr Ian Gibson, Labour MP for Norwich North and a microbiologist who chairs the Commons science committee, complained last night that too much unwarranted secrecy still surrounded the British decision. "There is no scientific evidence I have seen that one strain is better than the other. The American strain is probably better trialed, but it's all shrouded in secrecy. We don't know if the DoH or the MoD made the decision."

Dr Gibson's campaign to find out more is based on scientific curiosity, not a hunch that ministers were guided by a party donation. "The decision could have been taken on Rule Britannia grounds that it's a British strain," he admitted.