Latapy had been working with Caley manager John Hughes for the last 18 months, and the pair guided the club to victory over their former club Falkirk in the final of the William Hill Scottish Cup.
But he has decided to move on and is looking to move into management on his own account – he was linked with the vacancy at Alloa last season.
Latapy said: “My journey here has been fantastic and I have enjoyed every minute of my time in Inverness culminating in us finishing third in the SPFL and winning the William Hill Scottish Cup, a massive achievement for any club let all alone ICTFC.
“I have never hidden my ambition to one day be my own man in management terms and I believe now is the time.
“I would like to thank the supporters, players and all the staff for their support and co-operation during my time at the club including John for giving me the opportunity.
“I would also like to say I have enjoyed my time in the Highlands, it is a wonderful place to live and I have been made most welcome and have been extremely well treated by everyone at the club and the city of Inverness. I would like to wish the club and the team continued success in the future.”
Hughes could replace Latapy with former Falkirk and Hibs assistant manager Brian Rice who, according to reports in the Daily Record, has been in attendance at their recent pre-season matches.