"The person who carried out the first preparations for the assassination was a member of the armed forces," Mahmoud Alavi said in an interview with state television, without elaborating.
He said it was not possible for the intelligence ministry "to keep watch over the armed forces".
Mohsen Fakhrizadeh was travelling on a highway outside the capital accompanied by a security detail on November 27 when he came under machine-gun fire.
According to Iranian authorities, Fakhrizadeh was a deputy defence minister and carried out work on "nuclear defence".
Iran's elite Revolutionary Guards said a satellite-controlled gun with "artificial intelligence" was used in the attack, which Tehran blamed on its arch foe Israel.
The Jewish state did not react to the accusation but Israeli Prime Minister Benjamin Netanyahu said in 2018 that Fakhrizadeh headed a secret nuclear arms programme, whose existence Iran has repeatedly denied.
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