Mark Duggan cited personal reasons for his resignation, which sources say took place in late December.

His resignation came at the end of a tumultuous year for ACT's health system and was the most recent in a long line of high-profile departures.

Chief medical officer Jeffrey Fletcher quit in October after 18 months in the role, telling colleagues he would be looking for roles outside Canberra.

In September, Janet Anderson was announced as the new chief executive of the new organisation Canberra Health Services, created after the health department was split in two.

But just days later she pulled out of the job and in October was announced as the first commissioner for the new Aged Care Quality and Safety Commission.

Eventually, Victorian health bureaucrat Bernadette McDonald was announced as the interim chief executive and given the role permanently in December.

In March, ACT Health director general Nicole Feely resigned, at the same time the government announced it would split the department.

The medical imaging department has been the subject of an ongoing public interest disclosure submitted by a number of radiologists, alleging irregularities in Mr Duggan's recruitment procedures, and maladministration in the department.

The Canberra Times is not suggesting Mr Duggan's resignation is linked to the allegations.

The department has also come under scrutiny for its ongoing use of an external provider, instead of staff radiologists, for the reading of medical imaging scans.

It often uses the company Everlight to send images to doctors based interstate or even overseas to report on the images and send them back to doctors at the hospital.

Canberra Health Services said the practice was to address staff shortages mostly caused by unplanned leave.

Internal documents obtained by The Canberra Times revealed doctors believed the practice put people's lives at risk and contributed to poor outcomes for patients.

Invoices show the government spent $2,301,957 on the external provider Everlight last year, not including December.

The government could not provide the amount spent on external radiologists for December as the invoice had not yet been processed.

Canberra Health Services deputy director general Chris Bone said Mr Duggan resigned for personal reasons.

He said an interim director - a radiographer with managerial experience - had been appointed, with the search for a permanent replacement ongoing.

A senior radiologist has been acting in the separate role of clinical director since October 2018 - the third person to hold the role since April 2017.

The spokesman said three radiologists were recruited late last year and are now working in the department.

"We also interviewed several radiologists in December 2018 and we are in the process of completing this round of recruitment," he said.

"We intend to commence another round of recruitment in early 2019. This recruitment strategy will greatly reduce the need to use external agencies."

"Using an offsite radiology service for specialist reporting of diagnostic imaging studies is a recognised strategy in many hospitals.

"It ensures the continuity of person-centred, high-quality, efficient patient care at times such as after hours and when unplanned leave arises."