Alexander Rumyantsev's visit comes amid an intense diplomatic wrangle between Moscow and Washington over Russia's nuclear cooperation with a country that has been branded as part of an "axis of evil" by US President George W. Bush.
Russia has vigorously dismissed suggestions that its Bushehr project and other forms of military cooperation with Tehran were helping Iran developing a nuclear weapon.
Earlier this month, Washington identified two sites which it said were part of Iran's secret and nascent nuclear weapons program, and urged Moscow to take action.
But while dismissing US claims, Russia has struggled to secure an agreement with Iran that would guarantee the return to Russia of all the waste material from the plutonium supplied by Moscow to feed Iran's new Bushehr nuclear power plant.
RIA Novosti news agency reported that Rumyantsev would visit the Bushehr site during his stay in Iran.
Analysts say that while too low-grade to make an effective nuclear bomb, the waste could be used in a low-radiation "dirty bomb" that could still cause immense civilian casualties.
Russia has on several occasions reported that the nuclear waste agreement had already been struck, only to backtrack on its claims.
Rumyantsev said earlier this week that Russia had set the waste's return as a pre-condition for future nuclear cooperation with Iran.
"The return of nuclear fuel after its use (at Bushehr) is a firm condition for our cooperation with Iran," ITAR-TASS quoted him as saying.
The Bushehr project is worth an estimated 800 million dollars (779 million euros).