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Khamenei said in his Twitter post that Iranian officials must take up the task of 'pursuing this crime and punishing its perpetrators and those who commanded it.'
Fakhrizadeh has been described by Western and Israeli intelligence services for years as the leader of a covert atomic bomb programme halted in 2003, which Israel and the United States accuse Tehran of trying to restore in secret.
The 17 fishermen, hailing from Vizhinjam, Poovar and Pozhiyoor, in Thiruvananthapuram, were unable to move out due to restrictions imposed by authorities.
Tensions began rising in May when the US rushed thousands of additional troops, an aircraft carrier, nuclear-capable B-52 bombers and advanced fighter jets to the Mideast.