The expanded inquiry by parliament's financial watchdog is examining a second Powderject contract, which was also awarded by the Department of Health without rival bids and was criticised for being at a highly inflated price.

The NAO inquiry began after the row over the awarding of the smallpox contract, to accusations of sleaze, to Dr Drayson who has given £100,000 to Labour in the past year.

The inquiry will be the first comprehensive examination of how the government has awarded multi-million pound contracts to commercial companies to produce up to 10 vaccines to protect millions of Britons.

Auditors at the NAO have decided they need a proper benchmark to work out how vaccines contracts are handled by government .

Since April, the NAO has been scrutinising minutely ministers' claims that Powderject had to be given the lucrative smallpox contract because it was the only company which could deliver the required number of doses of the right strain of smallpox vaccine at the right time.

They plan to put their findings to all the rival companies involved in the smallpox "beauty contest" before Powderject was given the contract to see if the firms agree with the official version.

The government's conduct in the smallpox contract is being compared to its procedures in ordering the other vaccines. The Guardian has learnt that Department of Health officials have put up a vigorous defence of its actions over the smallpox contract to the NAO, arguing it was correct to prevent other firms from bidding.

Ministers claimed that open bidding would have revealed sensitive details about its plans to defend Britain against a biological terrorist attack. The NAO is to be given access to all the high security documents in the case.

But also coming under the NAO's scrutiny is Powderject's two-year, £17m contract to produce anti-tuberculosis vaccines for the Department of Health. Critics have pointed out that the contract, announced in March last year, cost the NHS four times what it had previously been paying.

Powderject was the sole bidder for the contract, as the Department of Health insisted it was the only manufacturer with a proper, British safety licence to produce the vaccine.

Powderject also has a contract to supply a flu vaccine to the NHS.

Whitehall has disclosed few details of the smallpox contract on national security grounds, but the NAO is believed to be pressing for as much as possible to be made public when it reports on its investigation, probably in November.

NAO officials and Whitehall civil servants are thought to be concerned that there would be political uproar if they produced a secret report which was then examined in private by the Commons public accounts committee.

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