Like a whale and the myriad barnacles clinging to its sides, Whole Foods Market and organic farmers have long had a symbiotic relationship.

The grocer has helped stoke the American appetite for organic products, building stores that are essentially showcases for organic fruits, vegetables and flowers tagged with the names of the farmers who grow them.

But that mutually beneficial relationship is now fraying, as Whole Foods faces increasing competition from mainstream grocery chains and as organic farmers find more and more outlets for their produce.

Now, some organic farmers contend that Whole Foods is quietly using its formidable marketing skills and its credibility with consumers to convey that conventionally grown produce is just as good — or even better — than their organically grown products. Shoppers can choose from fruits and vegetables carrying the designation of “good,” “better” or “best.”

The longtime suppliers to Whole Foods are complaining that the program called Responsibly Grown can grant a farmer who does not meet the stringent requirements for federal organic certification the same rating as an organic farmer, or even a higher one. Conventional growers can receive higher rankings than organic farmers by doing things like establishing a garbage recycling program, relying more on alternative energy sources, eliminating some pesticides and setting aside a portion of fields as a conservation area.

“Whole Foods has done so much to help educate consumers about the advantages of eating an organic diet,” five farmers wrote in a letter sent on Thursday to John Mackey, the co-founder and co-chief executive of Whole Foods. “This new rating program undermines, to a great degree, that effort.”

Tom Willey, who has been farming organically for more than 40 years in and around Madera, Calif., and others say the program is a subtle way of shifting the costs of a marketing program onto growers.

“The reports we’re getting from speaking to farmers around the country are that they are spending anywhere from $5,000 to $20,000 to comply with this program,” said Mr. Willey, one of the farmers who signed the letter.

The fact that Mr. Willey and other organic farmers, all of whom played significant roles in determining the federal regulations, are speaking out publicly is yet another indication of how much competition Whole Foods is facing from mainstream grocery chains like Safeway, Walmart and Costco, not to mention farmers’ markets and food cooperatives, which are booming around the country.