Iran has begun dismantling parts of its nuclear programme, as agreed in a landmark deal with major powers, the UN atomic watchdog has said.

Iran has started removing centrifuges and related infrastructureat the Natanz and Fordo enrichment facilities, the International Atomic Energy Agency quarterly report said on Wednesday.

The country had agreed to dramatically scale back its nuclear programme under the agreement reached on 14 July, ending a potentially dangerous decade-long standoff. These steps, coupled with increased UN oversight, are aimed at making it much more difficult for Iran to develop nuclear weapons, an aim it has always denied.

Measures include slashing by two-thirds the number of centrifuges, machines that can enrich or purify uranium to make it suitable for peaceful uses but also for a nuclear weapon. In addition, Iran pledged to change the design of a new reactor at Arak to reduce sharply the amount of plutonium produced, the alternative to uranium for a bomb.

In return, the six major powers – the US, Russia, China, Britain, France and Germany – have agreed to lift sanctions imposed on the Islamic republic. The accord was formally adopted by all parties on 18 October and it is expected to come into force in the coming weeks or months.

However, the IAEA report showed that despite taking out about a quarter of its roughly 19,000 installed centrifuges, Iran still has some way to go before all its commitments are met. So far, 4,500 centrifuges have been removed at Natanz and Fordo, the IAEA report showed, meaning it still has to take out approximately 10,000 more.

No preparatory work has taken place at Arak, the IAEA said, and Iran’s stock of enriched uranium gas has grown by about 460kg to about 8.3 tonnes (18,300lbs). Under the deal, this stock – which could in theory be purified to weapons-grade – has to be slashed to just 300kg.

The IAEA is also probing allegations that at least until 2003, Iran conducted research into developing nuclear weapons. The watchdog is aiming to compile a final report on these possible military dimensions of Iran’s activities by 15 December, although diplomats say it could be released earlier.

Iran says the allegations are false and based on bogus intelligence from the likes of the CIA and Israel’s Mossad.