By Annie Gasparro 

Whole Foods Market Inc. said sales growth slowed sharply last month following allegations that it overcharged customers in New York, contributing to another disappointing quarter for the natural-foods grocer.

Whole Foods said Wednesday that sales at established stores rose 1.3% in the three months ending July 5--its weakest growth since 2009 during the economic downturn. The company has struggled to keep customers amid tough competition from smaller imitators and big mainstream retailers such as Target Corp. that are stocking local and organic items.

Struggles at Whole Foods were exacerbated in the final weeks of the quarter after New York City officials found the company had mislabeled weights of freshly packaged foods like vegetable platters and chicken tenders, leading to overcharges of under $1 to nearly $15 an item.

Whole Foods co-Chief Executives John Mackey and Walter Robb made a video apology on July 1, saying the mislabeling was an inadvertent error by employees and that it also led to some incorrectly low weights.

The mislabeling fueled Whole Foods' image of being an overpriced grocer--something it has been trying to combat in recent years amid slowing sales growth.

The company said Wednesday it has since retrained its employees, and that the allegations involved only nine of its 425 stores, but that it had a national effect. "By any measure, it had a significant impact on our sales," said Mr. Robb. "If trust is broken, it has to be rebuilt a step at a time."

Whole Foods' stock fell 11% to $36.25 in after-hours trading Wednesday, as the company also issued fourth-quarter guidance that fell short of analyst expectations. Its shares are down 19% so far this year.

In the past two years, the Austin, Texas, chain has been lowering its prices to compete in a tougher era, after having the natural-and-organic-food market cornered for decades. It expected sales to take a hit initially, but believed it would attract more shoppers, eventually accelerating its growth.

But it still hasn't reached that turning point, said Edward Jones analyst Brian Yarbrough. "The growth rate has slowed massively," he said, "yet they are still opening more stores." He said the New York pricing issue isn't the only reason for its same-store sales growth slowing to 0.6% in the first few weeks of the current quarter.

"People are starting to lose faith in the management team," he said.

Mr. Robb contends that Whole Foods is starting to get its pricing right. It is opening a new line of stores next year called 365 by Whole Foods Market that it hopes will tap into a new set of consumers who are more value conscious, giving Whole Foods an additional avenue for growth.

The first one will be in the Los Angeles area in a location initially targeted for a Whole Foods store. Analysts have questioned how profitable the new 365 stores will be and whether they will significantly steal sales from the existing chain.

"In this rapidly changing marketplace, we believe we are taking the necessary steps to position ourselves for the longer term," said Mr. Robb said.

Whole Foods, which traces its roots back to the 1970s, says it can still triple the number of its U.S. namesake stores to 1,200 locations.

Overall for its quarter, Whole Foods posted a profit of $154 million, or 43 cents a share, up from $151 million, or 41 cents a share, a year earlier. Revenue rose nearly 8% to $3.63 billion.

Analysts surveyed by Thomson Reuters expected a profit of 45 cents on revenue of $3.69 billion.

For the current quarter, it projects profit of 34 cents to 35 cents a share with sales increasing by about 7%, compared with the consensus estimate of 38 cents a share in earnings on sales of $3.59 billion, or roughly 10% higher than the year-ago period, according to analysts surveyed by Thomson Reuters.

Maria Armental contributed to this article.

Write to Annie Gasparro at annie.gasparro@wsj.com

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