"We see that there are double standards and that one country is singled out while there is silence about Israel, which owns weapons of mass destruction," Mussa said after meeting a senior Iranian diplomat.
Mussa had held talks with Mohamed Sabhani, an Iranian foreign ministry official, who passed on a letter from Iranian Foreign Minister Kamal Kharazi about "efforts to set up a nuclear-arms free zone" in the Middle East.
"We are for equality in the application of international conventions," Mussa said, pointing out that Israel "is exempt from the nuclear non-proliferation treaty (NPT) while other countries are subject to pressure."
Unlike Iran, Israel has not signed up to the treaty, which allows international inspections of nuclear plants.
Iran warned Thursday of an international crisis if the UN nuclear watchdog, the International Atomic Energy Agency (IAEA), decided to refer the case of Iran's nuclear programme to the UN Security Council.
The United States has accused Iran of seeking to procure atomic weapons under cover of a civilian programme and has dismissed as "impossible to believe" an internal IAEA report saying there is no proof to that effect.