The exective director Laurence do Rego made an allegation last year that prompted an investigation into governance at the lender by Nigeria's securities regulator.
She told regulators last year that chief executive officer Thierry Tanoh pressured her to misstate the bank's 2012 performance, but said she had refused.
Her statement sparked the probe by Nigeria's Securities and Exchange Commission.
The bank said last year that do Rego, a long-time employee, had been suspended because she falsely claimed to be a qualified accountant.
Ecobank is working to shore up confidence in its governance in the light of the probe. It is viewed by investors as an African success story for its strong growth and expansion beyond its Togo base into dozens of African countries.
"Laurence do Rego, the Group Executive Director for Finance and Risk, is no longer an employee of the Company," said a brief statement from Ecobank Transnational Incorporated.
It gave no reason for her departure and a spokesman did not immediately answer a request for details. Do Rego declined to comment on Wednesday.