In a telephone call made by the Iranian president to Putin, "the need was underlined for all existing questions to be resolved in the IAEA (International Atomic Energy Agency) legal sphere through political methods," a Kremlin statement said.
Putin said he backed cooperation between Iran and the IAEA, including "in the resumption of the negotiating process."
The leaders' conversation came ahead of a key meeting in a month's time of the IAEA, a UN body monitoring nuclear proliferation.
The IAEA may decide to send Iran before the UN Security Council if no breakthrough in a standoff between the Islamic state and Western powers is achieved, diplomats say.
The United States and EU negotiators Britain, France and Germany fear Iran is secretly developing nuclear weapons and want it brought before the Security Council, which has the power to impose penalties such as trade sanctions.
But Russia, which has a lucrative contract to build Iran's first nuclear power reactor, has a veto on the council.
The IAEA's 35-nation board of governors in September found Iran in non-compliance with the nuclear Non-Proliferation Treaty, paving the way for the matter to be referred to the council if Iran does not halt nuclear fuel work and cooperate fully with an IAEA investigation.