Intelligence minister of Iran Heydar Moslehi made the allegation two days before Iran is due to resume talks with world powers seeking to resolve a long-running row over Tehran's atomic work.
Iran accused the International Atomic Energy Agency (IAEA) on Saturday of sending spies from foreign intelligence services to the Islamic state, underlining worsening relations between Tehran and the UN atomic watchdog.
Intelligence minister Heydar Moslehi made the allegation two days before Iran is due to resume talks with world powers seeking to resolve a long-running row over Tehran's atomic work.
"The IAEA has been sending spies working for foreign intelligence organisations among its inspectors, and it should be held responsible," Moslehi was quoted as saying by state broadcaster IRIB.
He was referring to IAEA inspectors who visit Iran regularly to monitor its atomic activities.
Moslehi repeated allegations that the intelligence services of Britain, the United States and Israel were behind the murder of an Iranian nuclear scientist this week, citing confessions from those arrested by Iran over the case.
The scientist, Majid Shahriyari, was killed in a bomb attack on his car on Monday.
"This terrorist act was carried out by intelligence services such as the CIA, Mossad and the MI6," said Moslehi. "A group that wanted to carry out a terrorist act but did not succeed, was also arrested. They confessed that they were trained by these intelligence services."
Ties between Iran and the IAEA have become increasingly strained under agency chief Yukiya Amano, who has taken a blunter approach towards the Iranian nuclear issue than his predecessor Mohamed ElBaradei.
Amano said in his first report on Iran in February that the IAEA feared Tehran may be working to develop a nuclear missile.
Iran has accused him of bias and ties soured further in June when he said Tehran was hampering IAEA work by barring some of its inspectors.
Iran has agreed to meet with a representative of world powers in Geneva on December 6-7 but it has made clear it will not negotiate about its "nuclear rights", code for sensitive work the West suspects is aimed at developing an atomic arsenal.
The powers — the United States, Russia, China, France, Britain and Germany — want Iran to curb its nuclear programme, which Tehran says is for purely peaceful purposes.
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