During the study, the Australian Public Service Commission looked at female public servants who took maternity leave in 2000-01 and whether they had been promoted by June 2007.
The data showed that 65 per cent of women who had taken maternity leave were not promoted in the six years after the leave, compared to 42 per cent of women without children, who did not receive a promotion over the same period.
"The latter group (women who did not take maternity leave) is significantly more likely to have been promoted by June 30, 2007," the commission said.
Although the commission did not examine the cause of the disparity but believes that it could be because it was more difficult to find part-time work at more senior levels.
It could also be due to mothers deciding not to seek more senior jobs because of the difficulties of balancing family commitments with the increased demands of more senior positions.
"The figures may also be distorted by the possibility that women having children are at a relatively more senior classification already and simply have less scope for promotion," the commission said.
National Foundation for Australian Women spokeswoman Marie Coleman also agreed that mothers were missing out on promotions because they were unable to be a senior manager and work part-time.
Equal Opportunity for Women in the Workplace Agency director Anna McPhee said the data documented what women already knew - "having a child brings a great opportunity cost to their career".
"I think it is certainly concerning that women are being discriminated against because of their family situation," News.com.au quoted her, as saying.
The agency's survey of 800 women found most of them wanted more responsibility at work, greater autonomy and promotion.