Figures compiled by the Australian Public Service Commission show rates of staff absenteeism at the Australian Digital Health Agency spiked last financial year as the government twice pushed back the end of the electronic medical record's opt-out period amid public concerns about privacy and data security.

Sick leave among ADHA workers reached an average of 14.2 days in 2018-19, the highest incidence among any Commonwealth agency, pushing the agency's overall rate of unscheduled absences out to an average of 17 days - well in excess of the average of 11.4 days across all agencies, and far above its absence rate of 11.5 days in 2017-18.

The agency said the Commission's unscheduled absence data only included the APS component of its workforce, and the overall result for all staff - both APS and non-APS - was an average of 9.6 days unscheduled absence.

"The agency has policies in place and an employee assistance program to support staff to manage health concerns, return to work following surgery and rehabilitation where required," the ADHA said.

The government moved to an opt-out model for the My Health Record early last year in an effort to boost the number of Australians registered with the scheme. People were originally given three months from July 16, 2018 to opt-out, but in August last year Health Minister Greg Hunt extended the deadline by a month, and then in November pushed it out to January 31, 2019.

In an assessment released on November 25, the Australian National Audit Office found that the implementation of the My Health Record's opt-out model was "largely effective", though management of shared cyber security risks was judged "not appropriate" and needed to be improved.

Following the implementation of the opt-out model, around 90 per cent of Australians now have a My Health Record, though participation among health care professionals is more limited.

Overall, rates of absenteeism in the public service have remained steady for the past three years at an average of 11.4 days a year - down from a peak of 11.6 days in 2014-15.

Other agencies to record above-average rates included the Clean Energy Regulator (16.8 days), ComCare (16.7 days), the Australian Research Council ((16.4 days) and Services Australia (16.4 days). The Future Fund Management Agency had the lowest rate (4.8 days), which the same as 2017-18. The fund's staff are employed on individual contracts rather than an enterprise agreement.