Two fishing vessels were detained by the Irish Naval Service and escorted into Dunmore East this morning.
It is alleged they were fishing for sprat without authorisation.
The two vessels were observed fishing in Waterford Harbour by the Fisheries Monitoring Centre.
The LE Ciara which was in the area was sent to investigate and boarded the trawlers.
Both were detained at around 10.30am after allegedly fishing for sprat.
Fishing for herring and sprat is prohibited on the South East Coast from September 20 to December 31.
The trawlers were escorted to Dunmore East and handed over to gardaí, which is normal procedure.
A spokesperson for the Irish Naval Service said: "During the boarding and inspection of the two vessels a minor confrontation occurred between the two fishing vessels and a number of local boats.
"It is alleged by one of the detained boats that his nets have been damaged," adding that "this is a civil law matter".