Speaking at a regional economic summit in Azerbaijan, Manouchehr Mottaki said Iran's nuclear activities would be better handled by the UN nuclear watchdog.
The United States, Britain and France circulated a draft resolution at the United Nations calling on Iran to suspend nuclear enrichment. The document will be legally binding if the council approves it.
Iran says its nuclear activities are peaceful. Washington says the programme could be a front for making weapons.
Mottaki said in English: "The Security Council is a place to secure the peace of all countries.
"Definitely international bodies should not avoid and ignore the essential rights of the countries and we hope that would not happen in the Security Council."
Mottaki was restating Tehran's long-standing opposition to its nuclear programme being referred to the council.
Russia and China, which hold vetoes in the council, have said they support action on Iran but want the resolution modified. They fear that too much pressure would be self-defeating and precipitate an oil emergency.
Dominique de Villepin, the French prime minister, said on Thursday that military action was not the solution to the stand-off.
The draft says countries should exercise vigilance to stop Iran obtaining nuclear-related technology and goods.
Russia, which is helping Iran to build a nuclear power station, has said it is opposed to any such restrictions.