Ali Akbar Salehi, who is also Iran's vice-president, said the new facilities would be built in the mountains to protect them from attack.
The UN nuclear watchdog last week said it was concerned Iran might currently be trying to develop nuclear weapons.
Iran's supreme leader denied the enrichment of uranium was for weapons.
Tehran has always maintained that its nuclear programme is peaceful.
But the US and other nations, which fear Iran is seeking nuclear arms, have been pressing for the UN to impose further sanctions over the issue.
Mr Salehi said the facilities would use new and more advanced centrifuges, according to the semi-official Iranian news agency Isna.
| || |
Iran says it is increasing uranium enrichment from 3.5% needed for commercial nuclear reactors
Iran says it has started enriching to 20%, needed for a medical research reactor near Tehran
Weapons-grade uranium is at least 90% enriched
Experts say achieving 20% is a key step towards weapons grade
The two sites are reportedly the first of 10 to be built in a plan announced by Iran's President Mahmoud Ahmadinejad last November.
The centrifuges might allow the Iranians to speed up the development of nuclear material.
Tehran has said it wants to enrich uranium to 20%, more than it has previously done.
The country says it is doing this to produce isotopes for medical use and to generate electricity.
But according to an unusually forthright report by the UN's International Atomic Energy Agency (IAEA) released last week, Iran's level of co-operation with the agency is decreasing, adding to concerns about "possible military dimensions" to its nuclear programme.
Iran's Supreme Leader Ayatollah Ali Khamenei said any fears were "baseless", as Iranians' beliefs "bar us from using such weapons".
Last year Iran revealed a previously unknown nuclear facility in the mountains near the city of Qom.
Previously it was believed that the only type of centrifuge Iran possessed were decades-old and in the the country's main enrichment facility at Natanz, which is monitored by the IAEA.
The facility near Qom had not become operational before its existence was announced.