I read food safety fairytales daily.

But as noted by Jesse Newman and Heather Haddon of the Wall Street Journal, supermarkets are starting to look a lot more like takeout restaurants, and the explosion of prepared meals has brought new food-safety issues that even leading chains are racing to manage.

Investors beware.

Whole Foods Market Inc., (which sucks a food safety) a trailblazer in the sale of fresh-cooked items, was recently forced to temporarily shutter one of its commercial kitchens producing fresh meals for stores. The move was a response to the U.S. Food and Drug Administration’s warning over safety gaps in the Boston-area plant.

The grocer is now overhauling its approach, including discontinuing the processing of meat, poultry and raw seafood in that kitchen and two others, according to a letter obtained through a public document request and the company.

The FDA’s warning followed an E.coli outbreak last year that was linked to rotisserie chicken salad made at Costco Wholesale Corp. and sickened 19 people. Deli foods from the Boise Co-Op, a natural-foods grocer in Idaho, were also tied to a salmonella outbreak last year that sickened nearly 300 people.

The grocers’ woes highlight challenges facing supermarkets competing for consumers forgoing home-cooking and traditional restaurant meals in favor of fresh offerings from sushi counters or taco bars at neighborhood grocery stores. As prepared-food offerings increase in volume and complexity, the risk of food-safety issues also grows, with supermarkets now facing safety concerns that have beset the restaurant industry for years.

Fresh prepared foods generated $15 billion in sales in supermarkets in 2005, a figure that has nearly doubled to about $28 billion last year, according to Technomic, a food industry research firm.

But while grocers have long offered fresh options from delis and salad bars, they now are selling more sophisticated meals, which require more complex cooking and serving practices.