ITAR-TASS said the talks were initiated by the Iranian side.
Russian officials have meanwhile confirmed that the country's top atomic-energy official will travel to Iran in February. Sergei Kiriyenko, the head of Russia's Federal Atomic Energy Agency, will hold talks on the Bushehr nuclear power plant, which Moscow is building for Iran.
Kiriyenko's spokesman, Sergei Novikov, told AP that he will also discuss Russia's proposal to enrich uranium for Iran's nuclear reactors in Russia.
Russia's ITAR-TASS news agency reported the Foreign Ministry confirmed "the situation around Tehran's nuclear program was the major theme of the [phone] conversation" between Ivanov and Iranian chief nuclear negotiator Ali Larijani.
Ivanov's office had earlier quoted the Security Council secretary as saying there was "no such conversation."
The United States and European Union have expressed concern about Iran's nuclear development program but both support a recent Russian proposal to enrich uranium for Iran's nuclear reactors in Russia then transfer the fuel to Iran.
Iranian officials said earlier this week that they had not received such a proposal from Russia.