Minister for Foreign Affairs Simon Coveney has expressed concern at the designation by Israel of six NGOs operating in the occupied Palestinian territories as terrorist entities.
Some of the six organisations receive funding from Irish Aid and the European Union.
Mr Coveney said the EU is in touch with Israel as they were not informed prior to the designation, which happened last Friday.
He said no detailed evidence had been provided by Israel.
In a statement, Minister Coveney said previous allegations against civil society organisations in the territory have not been substantiated.
"Ireland is committed to funding civil society organisations and human rights defenders through the Irish Aid programme, including Palestinian civil society, and maintains robust checks to ensure that our funding is used only for the purpose intended," Mr Coveney said.
He said terrorism was a very serious issue and that it "must be addressed with both resolve and with evidence".
"As stated by UN human rights experts in their statement of 25 October: 'anti-terrorism legislation is designed for a specific and restricted purpose and must not be used to unjustifiably undermine civil liberties or to curtail the legitimate work of human rights organisations'," the minister said.
He said the designation had the potential to affect these six organisations and to undermine vital humanitarian, development and human rights work.