The suspension followed a 12-day conflict between Iran and Israel, which saw unprecedented Israeli and US strikes on Iran's nuclear facilities and escalated tensions between Tehran and the International Atomic Energy Agency (IAEA).
Tehran has since said that future cooperation with the agency will take "a new form".
In a confidential IAEA report seen by AFP on Wednesday, the agency condemned Iran's "decision to suspend cooperation with" it as "deeply regrettable".
The Vienna-based IAEA said its decision to withdraw its inspectors from Iran due to safety concerns about military attacks on Iran's nuclear facilities was "necessary given the overall security situation".
In its report, it said that Iran has an estimated 440.9 kilogrammes of uranium enriched to up to 60 percent as of 13 June, when the conflict broke out. The sensitive stockpile is up by 32.3 kilogrammes since 17 May.
The IAEA cautioned that it had "lost continuity of knowledge in relation to the current inventories of nuclear material in Iran".
Uranium enriched to up to 60 percent fissile purity is close to the roughly 90 percent level needed for atomic weapons, and way beyond what its needed to generate electricity.
According to the IAEA, Tehran is the only non-nuclear weapon state to enrich uranium to 60 percent.
Iran has always denied seeking a nuclear weapon.
Tensions between Iran and the UN nuclear watchdog have repeatedly flared since a 2015 deal curbing Tehran's nuclear programme in exchange for sanctions relief fell apart.
Donald Trump unilaterally withdrew the United States from a landmark 2015 deal with Tehran during his first term as president. The deal had exchanged sanctions relief for limits on Iran's nuclear programme.
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