Somali officials at Bosaso airport insisted that the "heavy bags" on the flight be checked, resulting in an hours-long standoff.
It added that talks were under way between Somali's semiautonomous Puntland region and the UAE to end the dispute.
The UAE foreign ministry has not commented on the matter.
The news comes just days after Somalia's government seized several bags of money, loaded with almost $10million from a plane that arrived at Mogadishu airport from Abu Dhabi.
The money was found in three unmarked bags on a Royal Jet plane, the Somali interior ministry said, adding it was investigating where it came from, where it was going and the individuals involved.
"The security forces noticed the suspicious bags and handed them over to the concerned departments," Somalia's security ministry said in a statement.
Responding to the Somali action, the UAE had accused the security forces of holding those on the plane "at gunpoint", and said the cash had been allocated to support the Somali army and trainees.
Relations between Mogadishu and Abu Dhabi have been frosty since June last year after Mogadishu resisted UAE and Saudi pressure to cut ties with Qatar following a dispute between the Gulf neighbours.
