Chief Scientist Alan Finkel says the pay gap between men and women in science, technology, engineering and maths is unacceptable.
Women make up less than one-fifth of Australians qualified in science, technology, engineering and maths and continue to be paid less than their male colleagues.
It's a finding of a new report by the Office of the Chief Scientist, which shows 16 per cent of the 2.3 million STEM-qualified Australians are female, with engineering showing the largest gender gap.
When it comes to pay, 32 per cent of men hit the highest income bracket ($104,000), compared with 12 per cent of women in the latest Census.
Chief Scientist Alan Finkel said that could not be explained by women having children or working part time.
"The pay gap between men and women revealed in this report is significant, it is longstanding and it is unacceptable," he said.
"No clever country under-serves half its people."
The report, released on Thursday, found just seven per cent of engineers were women.
However, there were almost the same number of male and female scientists.
Based on the most recent figures from the 2011 Census, the report also found two-thirds of the STEM workforce earned qualifications through vocational education, with one-third university qualified.
It shows STEM-qualified Australians work across a diverse range of industries.
"We have people with physics doctorates working as financial analysts," Dr Finkel said.
"We have chemistry graduates running farms and making wines.
"There are no limits on what a STEM graduate can do, and we shouldn't impose them."
The federal government has earmarked almost $20 million to encourage primary and high school students to focus on STEM subjects.