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Sunday's remark by Intelligence Minister Heidar Moslehi is the first official number on the detentions. Last week, Iran announced it had made arrests linked to the slayings.
Moslehi claims the suspects moved between Iran and Israel through a neighboring country. He did not name the country, but Iran has accused Azerbaijan of harboring terrorists linked to Israel.
At least five Iranian nuclear experts have been killed since 2010. The US and Britain have denied any roles, but Israel has remained silent on Iran's accusations. In May, Iran hanged a man convicted in the killing of a nuclear physicist in early 2010.