Financial Ombudsman Service chairman Sir Nicholas Montagu said Ms Ceeney, an outspoken critic of poor practice in banking and financial services, would be moving on to new challenges. Deputy chief Ombudsman Tony Boorman will take the helm on an acting basis until a replacement is announced.
Ms Ceeney has overseen a huge expansion in the Ombusdman service's caseload since she joined.
Making the announcement today he said: "In the close to four years since joining, Natalie has taken the service from dealing with an annual workload of 150,000 cases to over 500,000 cases – with the organisation trebling in size under her leadership in response to the challenges of PPI.
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"So having just received our millionth new PPI complaint, Natalie feels that now is the time for her to move on – as the Ombudsman service itself starts out on a new set of challenges, building on the foundations for change laid under Natalie's leadership.
"The board and I are very grateful to Natalie for her achievements as head of the Ombudsman service – which under her leadership became a Sunday Times "top 100" best employer, resolving up to 2,000 consumer disputes a day."
Data published by the Financial Conduct Authority recently showed 2.9 million financial complaints were made in the first half of 2013, compared to 3.4 million consumer complaints reported by firms in the previous six months.