Cadbury's is using an out-of-date approach to risk assessment and product testing for salmonella contamination, experts advising the government say.
Cadbury said it would be changing testing procedures
The confectionery giant had to recall one million chocolate bars two weeks ago, amid fears that the products may contain a rare strain of the bacteria.
A government advisory committee said Cadbury's product testing was likely to underestimate contamination levels.
The firm said its testing procedures would be "improved".
BBC health correspondent Gill Higgins said experts were concerned other manufacturers may also have been failing to report problems and may have inadequate risk assessments in place.
The government's Food Standards Agency (FSA) sought the views of the independent Advisory Committee on the Microbiological Safety of Food (ACMSF) on the Cadbury's case.
ACMSF experts found failures in the company's methods of testing and risk assessment, with an over-reliance on end-product testing.
Cadbury's had failed to introduce adequate checks throughout the manufacturing process such as repeatedly looking for leaks in equipment, or checking cooking temperatures were high enough.
And they were wrong to assume even very low levels of salmonella were safe, the experts said.
In a statement, Cadbury's stressed that legislation left it up to manufacturers to determine testing protocols.
While it said its testing was based on sound science, it added that future procedures would be "improved" in light of FSA advice.
"At all times we have acted in good faith and we do not challenge the views of the expert committee advising the FSA," it added.
"We agree that it is their job to provide guidance on these matters and we welcome their advice.
"...We will move to a protocol in which we destroy any product evidencing contamination, regardless of level."
Cadbury's removed more than a million chocolate bars from shelves across the UK at the end of last month.
Samples were sent to an independent laboratory after a leak was discovered at its Marlbrook plant in Herefordshire, and the montevideo strain of salmonella was identified.
Cadbury's said the levels were "significantly below the standard that would be any health problem" but the recall had been carried out as a "precautionary measure".
ACMSF said: "The presence of salmonella in ready-to-eat foods such as chocolate is unacceptable at any level....
"Cadbury's risk assessment does not address the risk of salmonella in chocolate in a way which the ACMSF would regard as a modern approach to risk assessment."
Professor Tom Humphrey, of Bristol University Veterinary School - who speaks for the FSA - said the committee believed that, irrespective of what may be published, food like chocolate with a potentially large market of children should have no salmonella present.
"We do not accept the thesis that there's a safe level of salmonella in children.
"People vary in susceptibility, so if you're dealing in a product that goes to children, then we know from published evidence that children will be infected with lower levels of salmonella," he said.
During the ongoing investigation Cadbury's had revealed a previous contamination of its product with salmonella montevideo in April 2002 - but these products had been destroyed.
The committee said the company's risk assessment wrongly drew parallels between the threshold for salmonella infection and the threshold for infection by other micro-organisms which can be found in chocolate, when in fact there is no minimum infectious dose for salmonella.