The 61-year-old New Zealander and former Scotland head coach has stepped down for personal reasons after three years in charge.
"I'm disappointed to be leaving at this time," said Cotter, who led Scotland to the World Cup quarter-finals in 2015. "The team has made some significant improvements over the last few years both on and off the field.
"I would like to take this opportunity to thank the players and coaches I have worked with during my time with the team. I believe we built a great culture which was testament to some good people working hard and enjoying each other's company. I wish the team all the very best for the upcoming Rugby World Cup later this year."