"He decided to take new challenges in another industry other than shipping," according to a spokesperson for the Marseilles-based carrier.
The appointment of a new CFO will be announced in due course, the spokesperson said.
Schapiro was made an executive director of CMA CGM in January as part of a major management reshuffle following months of talks with creditor banks.
He is leaving at a critical time for family-controlled CMA CGM, which is seeking outside investors as part of a restructuring of its $5.3 billion of debt.
Jacques Saade, founder of CMA CGM, broke off talks with Qatar Holding earlier this week saying its conditions for a capital injection were too onerous.
Qatar's sovereign wealth fund was reported to have proposed a $1 billion cash injection in return for a 49 percent stake in the world's third largest ocean carrier.
Saade said he expects to reach agreement with a new investor by the end of July.