Whole Foods Market said the U.S. Securities and Exchange Commission is conducting an inquiry into Web postings involving the company, whose chief executive apologized to shareholders for his anonymous posts on financial message boards.
The company's shares fell 1.7% in extended trading following the announcement.
The natural and organic grocer also said its board of directors formed a special committee to investigate the postings.
"I sincerely apologize to all Whole Foods Market stakeholders for my error in judgment in anonymously participating on online financial message boards," Whole Foods Chief Executive John Mackey said in a statement.
SEC staff contacted Whole Foods late Monday, the company said, adding that it was cooperating with the probe.
Whole Foods hired Munger, Tolles & Olson to advise it in its internal investigation.