The latest IAEA quarterly report also said Iran had "significantly hampered" the agency's ability to inspect the Parchin military site. Iran has produced 189kg (417 lb) of higher-grade enriched uranium since 2010, it added.
Iran denies its nuclear programme has any military aspect.
The number of enrichment centrifuges at Fordo, at a facility buried deep inside a mountain near the holy city of Qom, had more than doubled to 2,140 from 1,064 in May, the IAEA said.
However, the new machines were not yet operating, it said.
Iran says the aim of the Fordo site is to enrich uranium for civilian use up to a maximum of 20%.
In May, UN nuclear inspectors found traces of uranium enriched at 27% at the site, but Iran said those readings could be accidental.
Analysts say 27% would bring Iran closer to making weapons-grade uranium.
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