The Health Protection Agency has been fined £25,000 for a spillage of the deadly bacterium E.coli 0157 at its centre in Colindale, north London.
Three employees were put at risk of contamination although nobody was infected, the Old Bailey heard.
Prosecutors described a "general complacency" about the way infectious waste was handled at the centre.
Judge Martin Stephens said the agency should feel "acute embarrassment" over its failings.
The bug was being carried in bins which had defects, even though these faults had been noted 18 months earlier.
Employees taking E.coli to a disposal unit were not wearing protective clothing, said prosecutor Andrew Marshall.
And there had been a "complete lack of understanding of risk" when an initial assessment of the spillage was carried out by staff, he added.
'Real' infection risk
Between 100ml and 200ml of liquid was spilt, containing up to 10bn E.coli organisms.
The agency pleaded guilty to a breach of health and safety laws and the incident was reviewed by the Health and Safety Executive.
One of its specialist investigators, Jennifer Higham, said the spill was a "serious breach" of the Health Protection Agency's duty "to ensure the health, safety, and welfare at work of all its employees",
"E.coli 0157 is a highly infectious and potentially-deadly bacterium and there are well-established practices for handling this safely," she added.
"But in this case, these practices were not met, exposing several staff and potentially their families to a real risk of infection."
The agency was created by the government in 2003 to act as an independent body which would protect the public from infectious diseases and environmental hazards.