There had been some doubt over the future of Cotter after Clermont president Rene Fontes told the club's website that the New Zealander had offered his resignation.
However, that was denied by Cotter, and following a board meeting, the club moved to clarify its position which will see the former Crusaders coach see out his contract.
A statement said: "The Board of Directors have unanimously approved the proposal of Jean-Marc Lhermet, athletic director and vice-president, to keep Vern Cotter in office for the sports season 2013/14.
"In this context, the ambitions of the club to do better than the previous season remain unchanged."
Cotter, who is not due to fully take up his position with Scotland until next summer, also made a statement on Clermont's official website to clear up any confusion.
He said: "My intention has always been to advance the club, never to harm anyone in ASM Clermont Auvergne.
"I regret having taken an awkward position vis-a-vis my players or club policy. There was clumsiness on my part and a lot of misunderstanding in a case that has been much more publicised that there should have been.
"I said with all stakeholders, I now have only one desire: to draw a line under last week and turn to the next season where we will have great ambitions.
"I'm going to New Zealand for 15 days to get new ideas, new lines of work to profit the club on my return. I am pleased that the club trust me for next season and I am very determined to finish my adventure in Auvergne beautifully."
- Sports & Recreation
- Vern Cotter