Massoud Hadian Dehkordi has said that there are currently 3,790,859 students in the country, of which he said about 50.5 percent are men and about 49.5 percent women.
Previously it had been reported, based on official figures, that women made up 60-65 percent of university entrants.
Some Iranian officials had expressed worry over the rising numbers of women at universities, and said that it represented a threat to traditional values and that it would limit women's marriage opportunities.
In 2008, the Research Center of the Iranian parliament expressed concern over the trend, which it described as "alarming" and called on the government to stop it.
The center said that over the last two decades there'd been a 23 percent increase in the number of girls taking university entrance exams, with the number of girls who passed the tests nearly doubling -- to 65 percent -- over the same period.
The government had proposed measures to stop the trend, including through the implementation of quotas for enrollment in some fields including medicine, where women were reportedly outnumbering men.
Women's rights activist Shadi Sadr says the new official figure of female students seems to suggest that efforts by Iran "to eliminate women from universities" have been successful.
"The most important policy is the policy of gender quota that has been implemented in the last five years in some fields, including medicine and engineering," Sadr told RFE/RL's Radio Farda.
"A limit is being imposed on the number of women who want to study in fields that are considered manly or the government believes that it is more [important] for men to study these courses than women."
Another policy that has been promoted, Sadr said, is pushing women to study at universities in their hometowns in provinces and smaller cities.
Officials have said in the past that the measures were not discriminating against women .
But women's rights activists have long protested against the moves, which they believe is a continuation of state repression of women and efforts aimed at keeping them at home.
-- Golnaz Esfandiari