"While their leaders see this as an advance, it is only a step backward... Instead of complying with the UN Security Council resolutions, Iran's actions may only lead them to more sanctions."
The IAEA note also said Iran had started up more than 1,300 centrifuge machines in an accelerating campaign to lay a basis for "industrial scale" enrichment in the Natanz complex.
The UN Security Council has demand that Tehran halt its enrichment programme over suspicions that Iran is using its civilian nuclear programme as cover to try to develop an atomic bomb.
Tehran insists its nuclear programme is intended only for generating electricity.
In the one-page letter – to Iranian officials from a senior IAEA staff member – a swift advance in Iran's nuclear programme is noted.
The US, UK, and France have criticised the announcement, but experts and several world powers have expressed scepticism that Iran's claims are true, claiming they are greatly exaggerated.
Two weeks ago, Iranian officials had said Tehran was running only a little more than 600 centrifuges, and had not introduced any uranium gas into them.
Last week, Iran heightened its claims by saying it had begun operating 3,000 centrifuges at Natanz - nearly 10 times the previously known number.
Mohamed ElBaradei, the IAEA director-general, had said that Iran was operating only several hundred centrifuges there.
"Iran has a right to pursue nuclear power but it should abide by international agreements and laws"
David, NYC, US
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However, the letter, signed by Olli Heinonen, the IAEA deputy director-general, said the agency wanted to "take note of the information provided by Iran ... that Iran has put into operation" 1,312 centrifuges.
The letter also cited Iranian information to the agency that "some UF6 is being fed" into the centrifuges, referring to the uranium gas that can be enriched to levels potent enough to be used for nuclear arms.
Iran says it wants to enrich only to lower levels suitable to generate nuclear power.
But suspicions about its ultimate intentions, after nearly two decades of nuclear secrecy exposed only four years ago, have led to UN Security Council sanctions for its refusal to freeze enrichment.
Experts say the successful operation of 3,000 centrifuges would make enough material for a nuclear warhead within a year.
Ali Ashgar Soltanieh, the chief Iranian delegate to the IAEA, said that his country had "no obligation to inform the IAEA".
He said Iran cannot accept Security Council demands that it suspend enrichment because they represent a "humiliation of the nation".
But he said the Islamic republic was ready to negotiate as long as the precondition of an enrichment freeze was dropped.