Mr Sharkie said he had enjoyed his time at the co-op and the challenges it provided.
"I am very proud of Ruralco’s achievements during my time at the helm," he said.
"It is the dedication and passion of the people who work for Ruralco that has made these achievements possible and I commend them for their efforts and wish them well for the future."
Chairman Sir David Carter said he had accepted Mr Sharkie’s decision with mixed emotions.
"Rob’s contribution to Ruralco has been significant, but I respect his decision that the time is right for him to pursue another chapter in his life. He leaves with my complete support and best wishes for his future endeavours."
Mr Aitken has a strong background in people leadership and was part of Synlait when it grew from 140 staff to a workforce of more than 1000.