Speaking alongside Gordon Brown and French president, Nicolas Sarkozy, at the G20 summit in Pittsburg, Mr Obama called on Iran to comply fully with the International Atomic Energy Agency (IAEA) and meet its international obligations.
"Iran must comply with UN Security Council resolutions and make clear its is prepared to meet its responsibilities as a member of the community of nations," Mr Obama said.
He added that Tehran would be held accountable for any failure to meet these responsibilities.
Mr Brown said news of the covert site had "shocked and angered" leaders.
"Iran's nuclear programme is the most urgent proliferation challenge that the world faces today," he said.
It was the third time Iran had been "caught red-handed" in breach of obligations over its nuclear programme, he added.
"The level of deception by the Iranian government and the scale of what we believe is the breach of international commitments will shock and anger the whole international community and it will harden our resolve," said Mr Brown.
He said the international community must now "draw a line in the sand" and threaten Iran with further sanctions in its talks with the E3+3 states - Britain, the US, France, Germany, Russia and China - in Istanbul on October 1.
"Confronted by serial deception over many years, the international community has no choice today but to draw a line in the sand," said the PM.
"On October 1, Iran must engage with the international community and join the international community as a partner. If it doesn't do so, it will be further isolated.
"I say on behalf of the United Kingdom, we will not let this matter rest and we are prepared to implement further and more stringent sanctions.
French counterpart Nicolas Sarkozy said the plant represented a "direct challenge" to international non-proliferation.
"This site deepens a growing concern that Iran is refusing to live up to these international responsibilities," he said.
The International Atomic Energy Agency said on Friday Iran had revealed the existence of the plant to IAEA Director-General Mohamed ElBaradei on Monday, just as six world powers and Iran prepare to discuss its disputed nuclear drive on Oct. 1.
The IAEA said Iran had told ElBaradei in a letter that the plant would enrich uranium only to a level needed to generate electricity.
"The agency also understands from Iran that no nuclear material has been introduced into the facility," International Atomic Energy Agency spokesman Marc Vidricaire said.
The agency requested specific information and an immediate inspection of the plant to ensure it was for peaceful purposes.
Iran was previously known to have one enrichment plant, a vast underground hall at Natanz where it has stockpiled low-enriched uranium in a rapidly expanding operation with almost 9,000 centrifuges installed.
Iran's ISNA news agency quoted an "informed source" on Friday as confirming the reports of a second uranium enrichment plant, saying it was similar to the Natanz plant.
The Natanz plant is under daily surveillance by IAEA inspectors. Iran concealed the site and other sensitive aspects of its enrichment programme from U.N. non-proliferation inspectors until the Iranian exiles blew the whistle in 2002.
It was not known how long the new plant had been under construction or planned. Iran stopped providing the IAEA advance information on nuclear site designs last year in retaliation for U.N. sanctions imposed over its nuclear campaign.
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