"Female and male students cannot live in the same house," the head of the Islamist-rooted Justice and Development Party (AKP) was quoted as saying by the Turkish press on Monday.
"That is contrary to our structure, which is conservative-democratic," Erdogan reportedly told party stalwarts at a weekend meeting in an Ankara suburb.
He added that his government would "one way or another supervise" the situation, the Radikal and Zaman dailies reported.
Erdogan, who has ruled Turkey for more than a decade, is accused of seeking to "Islamise" society with increasingly obvious references to Islam, and the remarks set off debate on social networks.
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Another, by Wim van Wegen, said: "The 'democratisation' of authoritative Erdogan's Turkey is a joke. Ataturk would turn over in his grave," a reference to the revered founder of secular Turkey in 1923.
A leader of the main pro-secular opposition Republican People's Party (CHP) demanded an explanation, saying: "Do you mean by 'supervision' that you also intend to monitor how students dress, like Iran's morality police do? Isn't this an attack on private life?"
Speaking before parliament, Umut Oran, a prominent CHP lawmaker, added: "Students are grown-up enough to make decisions about their lives."
Erdogan's government faced an unprecedented wave of protests in June over its repression of critics and growing imposition of Islamic values on Turks.