"It was a complex operation involving electronic equipment. There was no one at the scene, but we found clues. We know who planned this [attack] and we know their past," Ali Shamkhani said in a video statement.
The physicist died in a gun attack east of Tehran on Friday. Iranian media reported that he was shot dead with a remote-controlled machine gun.
Shamkhani added Iran had confirmed the role of the banned People's Mujahedin Organisation and the Israeli spy agency Mossad in the killing. Israel has not officially claimed responsibility for the shooting, which comes 10 years after the murder of another nuclear scientist, Majid Shahriar.