The oil-rich area declared its autonomy in 1998, and the region has had tense relations with the central government in Mogadishu.
Puntland forces intercepted the Comoros-flagged vessel, saying it had been observed "loitering" near the coast and could pose a security risk.
Mogadishu protested the move, calling it "an act of piracy", and said the ship was carrying equipment for a Turkish military base in the country as well as goods for Somali traders.
In a statement on Monday Puntland government said a Turkish delegation led by its ambassador to Somalia held a meeting in the region and provided "proof that all the property belongs to the Turkish government".
"Puntland government decided to hand over the responsibility of the vessel and the shipment it is carrying to the Turkish government," it said in the statement.
The semi-autonomous region said it had wanted to "ensure that the military equipment does not fall into hands that might threaten Somalia's security and stability."
Puntland launched an offensive in December against Islamic State forces present in the region.
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