Two years ago obstetrician Eftis Paraskevaides was suspended while a review of his work was carried out.
Five gynaecologists nominated by the Royal College of Obstetricians and Gynaecologists studied 562 patients' notes relating to Mr Paraskevaides' practice.
Concerns were raised in about 40 of the cases.
GMC investigation
His resignation from Hinchingbrooke Hospital in Huntingdon, Cambridgeshire, means that the independent inquiry into his work has now been stopped.
But the hospital, where Mr Paraskevaides worked for six years, has now referred the investigation to the General Medical Council.
On Thursday, Hinchingbrooke Health Care NHS Trust said it would make no further comment on Mr Paraskevaides' resignation.
A spokesman said in a statement: "The trust has referred the matters under consideration to the General Medical Council and, as these matters are not yet concluded by the GMC, it would be inappropriate for the trust to make any further comment."
The spokesman said that the majority of women who had been under the care of Mr Paraskevaides did not need to have any cause for concern about the treatment they received.
At the time of his suspension, the hospital said it was acting in the best interests of patients and set up a helpline to offer advice.
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