A statement said "the nuclear reactor in the area of Arak in Iran was targeted, including the structure of the reactor's core seal, which is a key component in plutonium production".
It said the strike on the site was carried out "to prevent the reactor from being restored and used for nuclear weapons development".
"Additionally, the (Israeli air force) struck a nuclear weapons development site in the area of Natanz," the statement added, saying that around 40 Israeli airforce jets had taken part in the overnight raids that saw "dozens" of sites hit.
Israeli Prime Minister Benjamin Netanyahu on Sunday said that Israeli forces had destroyed the principal uranium enrichment facility at the Natanz site.
The UN's International Atomic Energy Agency (IAEA) reported Tuesday that there appeared to have been "direct impacts" on the underground part of the facility.
Tehran has consistently denied seeking to develop a nuclear weapon.
Work on the Arak heavy-water research reactor on the outskirts of the village of Khondab began in the 2000s, but was halted under the terms of a now-abandoned 2015 nuclear deal struck between Iran and world powers.
Iran had informed the IAEA about its plans to commission the reactor by 2026.
The research reactor was officially intended to produce plutonium for medical research, and the site includes a production plant for heavy water.
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