A test tube containing the foot-and-mouth virus went missing from a top-secret laboratory two months before the outbreak was first recorded.

Now it appears that the disease which has crippled rural Britain could have been an act of sabotage by a rogue worker. The Ministry of Agriculture, Fisheries and Food was alerted when a sample of live virus was reported missing at Porton Down, Wiltshire, following a routine audit.

The test tube was stored in a highly sensitive laboratory where scientists also hold other details including smallpox, TB, ebola and anthrax.

The shocking revelation from the government laboratory undermines the ministry’s account of the rapid spread of the disease – yesterday it stood at 1,100 cases an increase of 20 and raises questions of a massive government cover-up.

It also supports documents seen by the Sunday Express, which clearly reveal that sheep in parts of the UK were carrying the virus long before the outbreak was confirmed on February 20.

According to a report by a French vet, it was detected in a Welsh flock as early as January.

Timber merchants around Britain say that in early February they were approached by the ministry for wood supplies to burn animals with foot-and-mouth.

Agriculture minister Nick Brown has told MPs the earliest known case was in a pig farm in Tyne and Wear on February 20.

He insisted the approaches were part of a "regular contingency planning exercise". He said: "There are a number of urban legends doing the rounds that the ministry knew about this disease before. This is not true."

Questions will be tabled in Parliament this week about the Porton Down link, and several MPs say they intend to give Mr Brown a "hard time".

Tory MP Owen Paterson said: "There are very persistant rumours over missing phials from Porton Down linked to animal rights activists.

"What I do know is that there is evidence that this disease has been round a lot longer than the government will admit.

"I specifically asked Nick Brown last week that if the outbreak was first revealed in February, then how come sheep exported from Wales to France were carrying the virus on January 31?

"He gave me a lame answer and also denied it. I know for a fact that a Mr Hugues Inizan exported sheep to France and they tested positive. Foot-and-Mouth takes a minimum of two to three weeks to incubate, so those sheep obviously had the virus a lot longer."

Tim Collins, Tory MP for Westmorland and Lonsdale, said: "If it emerges that the Government knew about a potential outbreak before the end of February, there will be an explosion of anger in my constituency."

Bob Parry, president of the NFU in Wales said: "We must get to the bottom of this mystery because no one has yet given a convincing explanation about the beginning of the outbreak.

"News of the stolen virus began circulating last week. Swill feeding is still being wrongly blamed. There is mounting evidence the disease started well before February."

A senior military source close to Porton Down said: " A phial appears to have gone missing from one of the labs following a routine audit last year.

"Ministry officials were informed immediately and an investigation was launched initially by Special Branch and then by MI5, who are interested in the activities of animal rights protesters."

Porton Down was rocked by scandal last year after samples of TB bacteria were wrongly sent to a Plymouth shop.

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