The US Federal Trade Commission has filed a lawsuit against the company to block its attempt to acquire rival grocer Wild Oats Market for $565m (£285m), arguing that the move would stifle competition and increase prices.
Whole Foods Market owns some 190 stores in the US and has recently moved into the UK market. It runs six Fresh & Wild stores in Bristol and London, and the flagship London branch of Whole Foods Market opened in Kensington last month on the old Barkers site.
As part of the investigation, Whole Foods Market chief executive John Mackey has admitted to hiding behind a pseudonym on the Yahoo! financial forum to talk up the success of his own company and spread rumours of the imminent decline of the rival organic grocer he was looking to acquire.
Mackey posted under the name "radhodeb" on the chat forum for seven years, between 1999 and 2006, but Whole Foods said the messages were personal postings and not connected to the company.
One message, posted by Mackey on the Yahoo! board in March 2006, read: "The writing is on the wall. The end game is now underway. Whole Foods is systematically destroying their viability as a business -- market by market, city by city."
Another read: "Bankruptcy remains a distinct possibility [for Wild Oats] if the business isn't sold within the next few years."
In a statement, Mackey said: "The views articulated by rahodeb sometimes represent what I actually believed and sometimes they didn't. Sometimes I simply played 'devil's advocate' for the sheer fun of arguing.
"All of rahodeb's postings also need to be understood in the context of the time that they were written. Because the competitive market has evolved so much in the last five years, older postings mean far less today than they did when they were written."