By the time they had been working for four years, males were earning around $47,760 while women were on $43,380 - a difference of $4380.
"It appears that there is an unequal benefit to tertiary education between males and females," said the report's author, Paul Mahoney.
When broken down by profession women working in performing arts were the only ones to earn significantly more - about $1400 a year - while those in information systems earned $10 more than their male counterparts.
The pay difference was up to nearly $8000 a year in some other professions. Female medical study graduates earned $6560 less than males, lawyers earned $4150 less, teachers $2400 less and women in communications and media earned $1730 less.
Mr Mahoney said one of the reasons men earned more than females may be link to a difference in the number of hours or weeks they work each year or the kinds of occupations and industries they work in.
"Where possible, future studies will test if this is the case."
NZ Union of Students' Associations national women's rights officer Caitlin Dunham said, "A lot of the time it's the fact that women have the risk of getting pregnant so will have to take time off. They will also be less likely to be in the line for promotion."
She said one problem was it was still "very taboo" to talk about how much you earned, while employers often placed the blame on women for not negotiating pay rises as well as men.
Equal Employment Opportunities chief executive Philippa Reed advised women to be informed about the going rates of pay and to ask for transparency when negotiating rises or promotions.
EARNINGS 4 YEARS AFTER GRADUATION
Computer science
Male $53,460 Female $51,270
Architecture and urban environment
Male$50,000 Female$47,830
Medical studies
Male$103,680 Female$97,120
Teaching
Male$45,670 Female$43,270
Law
Male$58,150 Female$54,000
Other society and culture
Male$45,170 Female$39,740
Visual arts and crafts
Male$39,300 Female$31,460
Graphic and design studies
Male$38,890 Female$36,540
Communication and media studies
Male$44,980 Female$43,250
Information systems
Male$50,560 Female$50,570
Performing arts
Male$30,840 Female$32,240
All bachelors completers
Male$47,760 Female$43,380