Security forces also reportedly found explosives in the bunker near the northern city of Isfara.
Officials from the prosecutor's office in the Sughd region told RFE/RL's Tajik Service that those using the bunker may also have connections with the banned Hizb-ut Tahrir group, as well as other militants fighting the Uzbek and Tajik governments.
The head of the prosecutor's office, Khairullo Saidov, said authorities had identified and were interrogating those suspected of using the bunker.
Another bunker was reportedly found late last year, also in Sughd, where security forces claimed to have confiscated a considerable number of leaflets and books calling for the violent overthrow of governments in Central Asia.