Three foreign trawlers are being held in the semi-autonomous Somali area of Puntland for fishing illegally.
Puntland official Abshir Abdi Jama said the boats were seized last week and denied reports they had been hijacked.
The Finnish ambassador in Kenya has denied initial reports that the trawlers are from Finland, saying he had been told they were from Egypt.
Piracy has been rampant in Somalia for many years, but stopped last year for several months under Islamist rule.
Earlier, Kenyan maritime officials expressed fears that the trawlers had been hijacked by pirates.
"The vessels captured belonged to some Arab and European countries and we have still not made contact with their governments," Mr Jama said.
Andrew Mwangura of the Kenyan based Seafarers Assistance Programme said their organisation had confirmed the vessels were being held in Puntland but was not aware how many crew members were in custody.
Last month, pirates set free a UN chartered ship, Mv Rozen after taking its crew - six Kenyans and six Sri Lankans - hostage for more than 40 days.
Since the overthrow of the Union of Islamic Courts in December insecurity in Mogadishu has deteriorated.
But interim government officials say they have now taken charge of the capital following days of battles with insurgents and Hawiye clan fighters opposed to the administration.
Maritime officials fear that the recent hijackings may signal a resumption of lawlessness on the seas.