The IAEA wants "more clarification" about the purpose of the Qom facility
President Barack Obama says the US and its partners are discussing "a package of potential steps" they could take if Iran snubs a uranium enrichment deal.
Mr Obama said Iran needed to get a "clear message" that, if it failed to take advantage of such opportunities, it was "making itself less secure".
Earlier, Tehran indicated it would not accept the offer to ship low-enriched uranium abroad in return for fuel.
It instead proposed carrying out a simultaneous exchange on its territory.
Correspondents say the proposal is very unlikely to be acceptable to the world powers negotiating with Iran over its nuclear programme.
The West fears Iran is attempting to develop nuclear weapons. Iran insists is nuclear programme is for entirely peaceful purposes.
A meeting of the UN Security Council's permanent members - Britain, China, France, Russia and the United States - plus Germany, will be held on Friday to discuss Iran's response.
On Monday, the UN's nuclear watchdog said it needed "more clarification" about the purpose of a recently declared uranium enrichment facility near the city of Qom.
The International Atomic Energy Agency (IAEA) also said in a new report that the development of the plant raised concerns about other possible secret sites.
On Wednesday, Iranian Foreign Minster Manouchehr Mottaki said his country had misgivings about the deal brokered by the IAEA in October that envisages Iran sending about 70% of its low-enriched uranium to Russia and France, where it would be processed into fuel rods for a research reactor in Tehran.
Mr Mottaki suggested a deal that the West and Russia are likely to reject
Mr Mottaki suggested Iran would instead agree to exchange its uranium for an equivalent amount of nuclear fuel, but only on its own territory. Tehran wanted to guarantee it would receive fuel it had contracted for, he said.
Responding to the comments, President Obama said the US and its allies had begun discussions "about the importance of having consequences".
"The dual-track approach requires Iran to get a clear message that, when it fails to take advantage of these opportunities, that it in fact is not making itself more secure, it is making itself less secure."
"Over the next several weeks, we will be developing a package of potential steps that we could take that would indicate our seriousness to Iran."
But Mr Obama said he still hoped Iran would change its mind.
"I continue to hold out the prospect that they may decide to walk through this door. I hope they do," he said.
"But what I'm pleased about is the extraordinary international unity that we've seen... I think it's an indication that we've taken the right approach."
NUCLEAR FUEL CYCLE
Mined uranium ore is purified and reconstituted into solid form known as yellowcake
Yellowcake is chemically processed and converted into Uranium Hexafluoride gas
Gas is fed through centrifuges, where its isotopes separate and process is repeated until uranium is enriched
Low-level enriched uranium is used for nuclear fuel
Highly enriched uranium can be used in nuclear weapons
Speaking during a visit to the Philippines, Mr Mottaki dismissed the threat of further international sanctions.
"Sanction was the literature of the 60s and 70s," he said.
"Well, in the last four years they have the experience of doing so. And I think they are wise enough not to repeat failed experiences. Of course, it's totally up to them," he added.
Mr Mottaki said Tehran was ready "to have further talks within the framework which is presented".
"It's not our proposal to have a swap," he added. "They raised such a proposal and we described and talked about how it could be operationalised."
Later, the Russian government insisted that there was still "every chance" of reaching a deal with Iran on enrichment, and denied that it was discussing further sanctions with Washington.
"As far as we know, there has so far been no final official answer from Tehran," Russian foreign ministry spokesman Andrei Nesterenko said in a statement. "It is important to let diplomacy work, and superfluous emotions only harm the situation."
"There is currently no discussion on working out additional sanctions against Iran at the UN Security Council," he added.
During Mr Obama's recent visit to China he received no assurances that it would support new sanctions against Iran at the UN Security Council. France and the UK want Iran to accept the deal.