Prof Threlfall warned that salmonella infections linked to ready-to-eat salads and herbs were rising, while other experts warned that such products could also be a source of E coli 0157 which can be fatal.
His warning sent shockwaves through the food industry, which has created a 400-million-a-year business selling bagged salads to Britons who lack the time to wash and prepare their own.
Representatives of the ready-to-eat salads industry expressed disbelief at Prof Threlfall's comments and maintained that there was no need to re-wash their products.
The HPA is a key government quango, issuing advice and monitoring UK public health issues and infectious diseases. It is a sister organisation of Health Protection Scotland.
Prof Threlfall, the director of the HPA's Laboratory of Enteric Pathogens - which monitors intestinal disease - said he wanted to alert the public about the potential risks when eating pre-washed salads.
"People could be putting themselves at risk by not washing these vegetables," he said.
"There have been a lot of outbreaks linked to ready-to-eat vegetables and herbs, often those shipped in from other countries."
In comments in the agency's magazine, Health Protection Matters, Prof Threlfall said: "Ready-to-eat products and fresh herbs are a common cause of salmonellosis, and these infections appear to be on the increase."
He highlighted a number of cases in the UK where prepared salad had been linked to outbreaks of salmonella, including 123 cases in 2004 linked to fast-food restaurants.
Last year, an E coli 0157 outbreak in the US was linked to baby spinach, leading to 205 infections and three deaths.
In the past year, there have been several cases in the UK where ready-to-eat salad bags have been recalled by supermarkets amid concern over possible salmonella contamination.
Prof Threlfall said salmonella cases were now "ubiquitous".
"Although the majority of infections in the UK are associated with raw food and are preventable by proper cooking procedures, ready-to-eat foods in various guises are responsible for an increasing number of infections," he wrote.
As well as cooking food properly and having good hand hygiene to avoid salmonella, the microbiologist said his "take-home message" for consumers was "to wash 'ready-to-eat' foods despite any instructions or implications (eg, 'already washed') to the contrary".
Prof Threlfall said he was sure there were more cases of salmonella linked to ready-prepared salads which were not identified because of the scale of food-poisoning incidents.
He said one source could be manure leaking on to salad crops, or put there on purpose to help growing.
The industry strongly denies that salads sold in the UK are grown using this practice.
Prof Threlfall said the cleaning processes to wash the salad used very dilute concentrations of chlorine, or just water, to protect the taste, but this meant some bugs could remain.
"We are trying to alert people about this," he said.
He said salad companies were aware of the problem and the HPA was in discussions with them about how to improve the situation.
"At the moment, the main message we are trying to put across is that ready-to-eat salad vegetables could have certain organisms on them and that you should give them a quick rinse before you eat them," Prof Threlfall said.
His comments were echoed by Scottish health experts. John Cowden, a consultant at Health Protection Scotland, said: "There have been cases of gastrointestinal disease linked to the consumption of salads. These have included not only salmonella, but also E coli 0157 and shigella, which causes dysentery.
"I personally would wash all salad items after buying them, particularly if giving them to someone who is very young, old, or otherwise vulnerable."
The Food Standards Agency (FSA) also agreed that extra precautions may be necessary with pre-washed products. A spokesman said: "Our advice is to wash all lettuce, including bagged lettuce, when you get it home.
"We will review this advice if we receive extra evidence and reassurances from the industry about their cleaning processes."
However, the Fresh Prepared Salads Producer Group, which represents UK salad companies, rejected the advice. Representative David Barney said: I am very puzzled by this advice. I don't understand why he is saying this and we would strongly argue against it. Our cleaning processes are robust and well-managed.
"The wash the salad gets is as good as any wash you would give in the home, and washing it again at home is not going to make a substantive difference to the safety of the product."
He insisted that manure was not used on any ready-to-eat salad products sold in the UK.
And he said that most incidents of food-borne illnesses linked to salads were caused by cross-contamination during the preparation process.
"There is almost no food-borne illness directly associated with retail prepared salads, because the washing systems have been particularly good."
Mr Barney said washing products again at home could actually make the problem worse. "It's widely known that kitchens - and particularly kitchen sinks - are the source of much cross-contamination," he said.
But campaigners continued to express concerns about the risks from pre-washed salads. Ishbel Mackinnon, the co-ordinator of E coli support group Haemolytic Uraemic Syndrome Help, said: "We are told that food wouldn't be sold unless it is was safe as it can be. But given the devastating effects of diseases like E coli 0157, if taking precautions means doing something twice, then it should be done twice.
"It will give you more peace of mind that you are doing everything you can to safeguard your family."
Lisa Miles, a scientist with the British Nutrition Foundation, said some people found pre-prepared salads a convenient way to increase vegetable intake, as it was a way of grabbing a healthy meal on the go.
"But preparing your own salad from fresh, which involves the washing of the salad yourself, is often cheaper," she said.