The Minister for Defence, Mr Smith, vetoed a request from his Cabinet colleague, the Minister for the Marine and Natural Resources, Mr Fahey, for representation at last week's crisis meeting over monitoring of Irish fishing vessels.
Mr Fahey had sought Naval Service attendance at the emergency talks with fishing industry representatives in Castletownbere, Co Cork, last Thursday.
The meeting had been convened in the wake of protests by fishermen in both Castletownbere and Dingle, Co Kerry, over surveillance of Irish fishing vessels.
However, Mr Smith overruled the invitation, having remained silent on the controversy throughout the past week. It is understood that he regarded participation as "inappropriate".
Shortly before the row erupted - sparked off by the detention of a fourth Irish tuna boat in a month - Mr Smith had dismissed fishermen's claims that the tuna fleet was being targeted by the Naval Service. He was speaking to reporters before his first trip on the new patrol ship, LE Roisin.
Four days later, his colleague, Mr Fahey, acknowledged that he had directed that the Irish tuna fleet be monitored. He also said he intended to seek greater surveillance of other EU vessels.
After the meeting in Castletownbere, Mr Fahey denied there was any tension between the two departments.
Meanwhile, the Naval Service recorded its 30th detention this year at the weekend, with the apprehension of a Norwegian vessel. The Kamara was detained 80 miles north of Achill for allegedly not having a fishing licence or a special permit to fish in Irish waters. It was escorted to Galway by the LE Ciara where it was handed over to the Garda.
