By Pallab Ghosh
BBC News, Science correspondent
Facilities at the laboratory are being redeveloped
A government review of the Institute for Animal Health at Pirbright five years ago found deficiencies in the standard of some of its laboratories.
The review carried out for the Biological and Biotechnology Research Council in 2002 said the institute "was not commensurate with what might be expected for work with infectious diseases".
And the review authors said they were concerned that some areas were "shabby".
Questions were also raised about the loss of "key skills" at the laboratory as senior personnel left and were not replaced.
On Sunday morning the head of the laboratory, Professor Martin Shirley said that building works were under way to improve the quality of the facilities.
He also said that vaccine was present on the institute site - and there had been limited use of it within the past four weeks - but proper procedures had been followed.
"The IAH operates under strict biosecurity procedures licensed by Defra," said Professor Shirley.
"In addition to general checks on biosecurity, operation of equipment, procedures and physical barriers, which have shown no breaches of our procedures, we have been able to check our records specifically for use of this strain.
It is highly unlikely that the exact same strain of foot-and-mouth virus that was being kept in the Pirbright facility would have emerged spontaneously in the wild - just a few miles away.
The question now for health and safety inspectors is which of the two laboratories on the Pirbright site might the virus have emerged from?
Professor Martin Shirley has defended the laboratory's facilities
The inspection team is looking at the facility that is commercially run by Merial first because it contains much more of the infectious agent.
But small amounts were kept at the adjoining publicly run Institute for Animal Health. Five years ago a review of the institute found some labs were not fit for purpose for dealing with infectious diseases.
Some scientists have criticised the government for not including the laboratories in the exclusion zone straight away - because they say it was obvious that they were a potential source of the infection.
The HSE are expected to report initial findings within the next 48 hours.