Iran "strongly protests against such unlawful acts and emphasises the necessity to observe the principles of international law concerning the sanctity of the sovereignty and territorial integrity of states", its Foreign Ministry said on Monday.
The Pentagon had no immediate comment to the protest, which came in letters to the US government written months ago but only made public at the UN on Monday.
They described the crash of a Shadow 200 RQ-7 drone in Ilam province on 4 July, 60km from the border, and of a Hermes drone in the Khoram Abad area on 25 August, found 200km inside Iranian territory.
An investigation found that both of the unmanned aircraft were American, the Foreign Ministry said.
Its letters were delivered to the Swiss Embassy in Tehran for transmission to US authorities as Iran has no diplomatic ties with the US.
US President George Bush insists that Iran is pursuing weapons of mass destruction under the guise of a peaceful nuclear energy programme.
Iran has denied the accusations and says its nuclear programme is designed to meet its growing energy needs.