The level of enrichment indicated in the letter would mean Iran was enriching uranium to a standard for use in nuclear power plants, but not in nuclear weapons.
'In response, the IAEA has requested Iran to provide specific information and access to the facility as soon as possible,' IAEA spokesman Marc Vidricaire said.
'It's catastrophic,' said Andreas Persbo, a London-based nuclear arms control expert, reacting to the revelations.
'It just shows that the worst fears of hawks in Western intelligence agencies have come true,' he said.
A number of nuclear arms experts have described a scenario in which Iran would use a secret installation to make material for a nuclear bomb, while letting the world believe the known Natanz site is the only enrichment facility it has.
The UN Security Council has applied three rounds of sanctions on Iran in an unsuccessful effort to get the country to stop its enrichment activities at Natanz.
'One would have to judge this as a determined signal from Iran to press on, despite what the six countries or the Security Council says,' a European diplomat said.
The diplomat briefed on Western intelligence said the plant was unlikely to start operating before next year, while another diplomat said it seemed Iran would need at least six months to start running the facility.
Construction at the Qom site likely began two years ago, Persbo said, adding that there had been talk about a possible secret nuclear facility among London diplomats and experts for quite some time.
According to the IAEA, no nuclear material has likely been introduced at the newly disclosed location, and a diplomat said no equipment for enrichment had been installed yet.
All diplomats speaking with DPA demanded anonymity because they were not authorized to speak on the record.