Welcoming Iranian nuclear negotiator Saeed Jalili at his residence outside Moscow, Putin said all of Iran's nuclear programmes must be "transparent" and under the supervision of the International Atomic Energy Agency (IAEA).
"We are very pleased that contacts between Iran and the IAEA have been stepped up," Putin was quoted by news agencies as saying.
"We welcome the expansion of this cooperation."
Putin earlier received a telephone call from US President George W. Bush that touched on Iran's nuclear programme, Interfax reported quoting a Kremlin official.
A report issued on Monday by the US intelligence community corrected previous US administration allegations that Iran was actively seeking to develop a nuclear bomb.
The report said the programme had been shut down in 2003 and had not been re-started since.
Putin said he hoped that "all Iranian programmes in the nuclear sphere will be open and transparent and will be carried out under the control of this international organisation."
"In bilateral relations our cooperation is intensifying in almost all sectors," Putin said.
Russia is helping Iran build a nuclear reactor and has repeatedly said it has no evidence that Iran is trying to build nuclear weapons as alleged by the United States and its European allies.
An IAEA team on Friday completed five days of inspections of the first consignment of Russian fuel to be shipped to Iran's nuclear power plant at Bushehr.
In his remarks at the outset of his meeting with Jalili, Putin made no reference to the US report and simply reaffirmed that cooperation with the IAEA would clear up suspicions over Iran's nuclear activities.
IAEA director general Mohamed ElBaradei said the new US assessment "should help to defuse the current crisis" over Iran.
In October, Bush had raised the spectre of "World War III" or a "nuclear holocaust" if Iran obtained an atomic arsenal.