The Foreign Ministry did not disclose the content of the seizure, but the U.N. sanctions against Iran ban the export of arms and prohibit nuclear enrichment.
Turkish media said Wednesday the plane was carrying light weapons, including automatic rifles, rocket launchers and mortars.
Turkey says the plane, which had landed in the southeastern city of Diyarbakir on Saturday for the search, returned to Iran Tuesday night without the seized cargo.
The government says it routinely searches Iranian cargo planes flying over Turkey.