The oil-rich area declared its autonomy in 1998, and the region has had strained relations with the central government in Mogadishu.
Puntland forces intercepted the Comoros-flagged vessel last week when it was transporting military equipment to Turkey's Camp Turksom in Mogadishu, Ankara's largest overseas military base and training facility.
The government said the "hijacking" of the vessel was "carried out by individuals affiliated with the Puntland State" and was a violation of the constitution, adding it "constitutes an act of piracy."
According to Mogadishu, the ship was carrying legally authorised military cargo, along with commercial goods belonging to Somali traders. It did not give further details.
Last week, sources told AFP the vessel was seized after a technical hitch forcing it to move closer to Puntland's coast.
Fishermen near northeastern Bareeda town saw the stalled ship and called Puntland coastguards who boarded and inspected it, said police officer Abdullahi Ahmed.
A day after the ship was seized on July 19, Puntland said it had "unlawfully stayed at the coast of Bareeda... for two days without sending a distress call," as required by law.
The Ministry of Information said the vessel was carrying a visible armoury "that can pose security threats".
"It is worth mentioning that the ship stayed at one of the zones of the war against the international terrorists, which poses further risk to the stability and security of Puntland," the ministry said.
Bosaso city sources told AFP the ship remains docked, and that investigations are ongoing.
Somalia has vowed to take "lawful security measures" to safeguard its maritime zones and that it will not accept "any action that endangers the sovereignty of the nation or the security of its waters".
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