“Iran has conveyed its protest to Somalia in this regard through relevant channels,” Bahram Qassemi told ISNA on Wednesday.
He added that the Iranian Foreign Ministry was seriously following up on the issue.
Last week, Somali regional officials said the incident took place after security forces opened fire on the vessel during an operation in the Indian Ocean, according to reports.
The officials claimed the shooting took place after maritime police forces in Puntland, an autonomous region in northeastern Somalia, spotted two boats suspected to be fishing illegally Friday in Somali waters.
Colonel Mohamed Abdi Hashi of Puntland police said security forces opened fire on the boats when they ignored orders to stop and attempted to escape, adding that one boat was seized while the other fled.
According to the official, 16 other crew members were unharmed and apprehended.
He said he was not sure if Somali political leaders had made any contact with Iran about the incident.