Kirgotty was said to have been fighting for a renewal of his contract but that was not forthcoming.
He has recently been in the media talking about enhanced payments by the Fund for different conditions that patients go to hospital with.
The Finance Director Geoffrey Gitau Mwangi will act until a CEO is appointed.
This is even as some within the Fund call for a lifestyle audit of the FD.
Kirgotty's last day of service was said to be Friday last week.