The Department of Defence has confirmed two Northern Irish fishing boats were detained earlier this week.
Naval vessel LÉ Orla was deployed to Dundalk Bay on Tuesday.
Two UK-registered boats were detained in relation to alleged breaches of fishing regulations.
In a statement, defence officials said: "Following a routine operation, the vessels were escorted by the LÉ Orla to Clogherhead and were handed over to An Garda Síochána.
"For comparison purposes, the Naval Service detained 7 fishing vessels in 2018 of which two were UK registered fishing vessels."
The alleged offences relate to "vessels illegally fishing within the Exclusive Fishery Limits of the State" and "illegal entry into the Exclusive Fishery Limits of the State at a time when prohibited so to do".
The impounding of the Northern Irish fishing boats was sharply criticised by deputy DUP leader Nigel Dodds.
The Irish Prime Minister must explain why two Northern Ireland trawlers have been impounded by an Irish Navy warship.
I have already raised the matter with our Government.
These heavy handed tactics show Ireland are fair weather friends to NI. https://t.co/aQax4hiuge
— Nigel Dodds (@NigelDoddsDUP) February 28, 2019
In a statement, he claimed: "Whilst Northern Ireland allows Irish boats to fish in our waters, the Republic of Ireland has policed a hard border and do not allow Northern Ireland boats enter their waters.
"This is quite outrageous."
Mr Dodds added: "These heavy handed tactics with our fishing vessels demonstrate that Leo Varadkar and Simon Coveney are entirely focused on Ireland and are fair weather friends to Northern Ireland."
Fishing between the two territories has been based on the Voisinage Agreement - an informal deal allowing boats from both countries to fish in each others' territorial waters.
However, the deal collapsed due to a Supreme Court order in 2016 - shortly after the Brexit referendum.
The Government has previously indicated it plans to give the informal arrangements "a proper legal footing", while the UK government has continued to recognise the informal deal.