Armer, who has been on the dairy co-operative’s board for six years, was previously tipped to succeed the current chairman Sir Henry van der Heyden, who recently announced who would replace him later this year.
Last week, van der Heyden announced that John Wilson had been elected by the board as the Chairman elect. Wilson will take up the role when van der Heyden stands down as Chairman in December 2012.
“While we are disappointed that Colin has chosen to resign we respect his decision,” a Fonterra statement said.