"Today, students should shout at the president and ask why liberal and secular university lecturers are present in the universities," the official Islamic Republic News Agency quoted him as saying during a meeting with students.
Ahmadinejad complained that reforms in the country's universities were difficult to accomplish and that the education system had been affected by secularism for the last 150 years.
But, he added: "Such a change has begun."
It was not clear if Ahmadinejad intended to take immediate specific measures, or if he was just urging the students to rally.
Since taking office a year ago, Ahmadinejad has also moved to replace pragmatic veterans in the government and diplomatic corps with former military commanders and religious hardliners.
Earlier this year, dozens of liberal university professors and teachers were sent into retirement, and last November, Ahmadinejad's administration for the first time named a cleric to head the country's oldest institution of higher education, Tehran University - drawing strong protests from students.
His administration has also launched crackdowns on independent journalists, websites and bloggers.
The latest call seems to be another sign that Ahmadinejad is determined to remake Iran - which still has strong moderate factions - reviving the fundamentalist goals pursued in the 1980s under the late Ayatollah Ruhollah Khomeini, father of the 1979 Islamic revolution in Iran.
Shortly after the 1979 revolution, Iran fired hundreds of liberal university teachers and expelled numerous students.
It had a brief period of reform in the 1990s under Mohammad Khatami, the then-president but hardline factions cracked down then too, especially on university students, dissidents and journalists.
Ahmadinejad's targeting of academics seen as liberal is apparently similar to moves in the US, where conservatives have been lobbying against liberal university professors, calling for students to report unpatriotic positions or rhetoric, since the September 11, 2001 attacks.