Luis Fernandez has left his role as Guinea coach only one week before the team will play a vital Africa Cup of Nations qualifier away to Swaziland.
He told French radio: "It is a termination of contract by mutual agreement after the changes at the head of the Guinea federation.
"There have been many changes since I arrived but I leave as a good friend."
Fifa last month appointed a committee to take over the running of the Guinea Football Federation (FGF).
It followed what world football's governing body described as "internal wrangles affecting the FGF that have halted all football competition in Guinea".
Guinea are three points behind leaders Zimbabwe in Group L of the qualifiers for the 2017 finals in Gabon with two rounds to be played.
An away win over Swaziland on 5 June would keep Guinea in the race to win the group as they finish the qualifiers with a home game against Zimbabwe in September.
Fernandez, a former France international, was appointed in April 2015 and tasked to help the team qualify for the 2017 African Nations Cup and the 2018 World Cup.