Sohrab Razaghi, the director of the organization Koneshgaran, was taken into custody on October 24 and transported to an unknown location.
Officials have told Razaghi's family to follow up his case with the country's Islamic Revolutionary Court, which generally targets individuals suspected of acting against the country's leadership.
Neither the reason for his detention nor the charges against him are clear at this point.
Colleagues told Radio Farda that Razaghi had been summoned to the Intelligence Ministry several times before his arrest. Razaghi was previously detained in March and his offices shut down.
Razaghi -- a former professor of political science at Tehran's Allameh Tabatabai University -- was reportedly dismissed from his job in academia when President Mahmud Ahmadinejad came to power in 2005.
Ahmadinejad has urged university students to push for the removal of liberal-minded professors. This year has seen an increased crackdown on intellectuals, activists, and human rights defenders.
Another prominent rights activist, Emad Baqi, was detained and jailed in Tehran on October 14.
Shirin Ebadi, a Nobel Peace Prize winner and head of the Tehran-based Center of Human Rights Defenders, told Radio Farda that Baqi's arrest is the latest sign of mounting government pressure on civil society.