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Women are losing the battle for equal pay with recent female graduates earning almost 10 percent less than their male counterparts, a study by the federal government's Workplace Gender Equality Agency has revealed.

The pay gap between male and female graduates more than doubled from $2000 to $5000, with men earning a median wage of $55,000 last year, up from $52,000 in 2011.

Female graduate's median wage stayed unchanged at $50,000 across both years, leaving a 9.1 per cent gap between male and female pay rates in 2012.

Report author Dr Carla Harris said workplace culture and subconscious bias could contribute to unequal treatment during recruitment.

"In some organisations there is often a bit of a boy's club," Dr Harris said.

"Sometimes there is embedded bias, it may not always be conscious, but often we will preferentially treat different types of people - like attracts like, ... and people tend to recruit people similar to them," she said.

The pay gap between a young woman and man's starting salary in the field of dentistry could be as high as $14,400, according to Dr Harris.

The difference was most pronounced in the architecture and building industry, where male graduates take home a 17.3 per cent higher median pay packet than their female colleagues. Optometry had an 8.5 per cent gap, and law 7.8 per cent in favour of men.

The report found seven industries, all science related, where women graduates earning higher salaries, but the gap was smaller.

The highest discrepancy was in pharmacy where female graduates could earn just over 10 per cent more than men.

Dr Harris said there may have been a concerted effort by certain sectors to get women into them, but overall men were still earning more across more industries.