Dr Prosper Akanbong will be replaced by Dr David Zaawumya Kolbila, who is a gynaecologist and a lecturer at the University for Development Studies Medical School.
Dr Akanbong was appointed in September 2014 to succeed Dr Ken Sagoe at the time.
According to Accra-based Class FM, there was confusion on Monday during a handing over ceremony as Dr Akanbong raised issues about the manner in which he was being asked to leave.
Reports say a letter written to that effect did not state what his fate will be after he leaves office.
He has, therefore, indicated that he will not leave office until he is given a letter which will clarify his status after he leaves.