Mr Pflanz, who was the company's finance director when it bought the Islay distillery for £58 million in the summer of 2012, had been appointed chief executive in June, and formally took the top job on October 1.
Remy Cointreau had warned of a fall in profits, which it blamed on a slowdown in China, when it updated investors in November.
Board chairman Francois Heriard Dubreuil will act as chief executive, the company said, adding that its strategy remains unchanged.
Remy Cointreau said Mr Pflanz would remain within the company as development director.
A former finance director at the consumer products unit of cosmetics giant L'Oreal, Mr Pflanz had been Remy's finance director since July 2010. He added the chief operating officer post to his duties in December 2012.
Mr Pflanz took over the chief executive role from Jean-Marie Laborde, who had led the firm for nine years and was the driving force behind group's focus on high-end brands such as Remy Martin cognac and its move into Scotch whisky.
Bruichladdich, which was established in 1881, is renowned for the large range of whiskies, including the highly peated Octomore brand.
Its latest marketing has made much of the provenance of the barley used to make its spirit.
Shares, which trade on the Euronext, closed the day down 2.56% at 58.91 euros.