The chief executive's pay comes with the difficult task of overseeing the $156 million agency and its remit to digitise the nation's health systems, including fixing the delayed national roll-out of My Health Record.

Despite a number of teething problems, about 4.4 million Australians have signed up so far, as the government moves towards an "opt-out" system rather than the previous "opt-in" system.

The government's creation of an agency dedicated to improving digital health systems was been widely supported, although some stakeholders have been sceptical of how much the agency will achieve given past problems.

Health Minister Sussan Ley, who has since been stood-aside amid a growing expenses scandal, has previously described the use of digital technologies in health as "a game changer".

She said in a speech last year the agency's approach would be "whole-of-system, integrated and strategic" with "a focus on clinical quality and safety, and real engagement and collaboration with consumers, healthcare providers and industry".

A health spokeswoman said the new chief executive, Tim Kelsey, was appointed after an exhaustive recruitment drive including reviewing more than 100 applications from around the world.

"The short-listing and interview process was chaired by the chair of the agency's board, and the committee included senior Commonwealth and state health officials, and another of the agency's board members," she said.

"State and territory health secretaries were also consulted and provided positive support."

The agency's board includes chairman Jim Birch, also chairman of the Australian Red Cross Blood Service; Paul Madden, the department's "strategic health systems and information management special adviser" and Stephen Moo, Northern Territory Health's chief information officer and chairman of the National Health Chief Information Officer Forum.

Mr Kelsey brings extensive experience in digital health systems to the role, including leading the design of "a new national strategy for data and technology in his capacity as the first chair of the National Information Board", she said.

"Mr Kelsey designed and launched Europe's most visited online health information service – NHS Choices – which has 50m unique users each month," she said.

"He was also founding CEO of Dr Foster, a business in the UK that pioneered online data analytics in healthcare."

However, it is understood there were major problems with protection of people's privacy with another UK initiative Mr Kelsey oversaw, Care.data, which recorded patient's health records in a digital system.

The salary for the role, determined by the federal government's independent Remuneration Tribunal early last year, makes it the highest-paid role overseeing any federal health agency, outside of those paid to the most senior executives in the Department of Health.

It provides a base salary of $365,570, as part of a total $522,240 package, for the five-year statutory appointment, level-pegged with the Australian Electoral Commissioner and Commonwealth Director of Public Prosecutions salaries.

But it exceeds other leaders of federal health agencies, including the chief executive of the Australian Commission on Safety and Quality in Health Care, on $292,460 base salary and a total $417,800 package.

It also exceeds the chief executive of the National Mental Health Commission, a position that attracts a $247,810 base salary as part of a $339,460 total package.

The department's spokeswoman said the overall package was "based on consideration the role and accountability of the CEO position, the skills and experience required of the occupant and the remuneration of similar positions across government, including roles in health and those outside of the health sector".

"The selection process was merit based and was conducted in line with the Australian Public Service Commission senior executive service selection guidelines," she said.