Forty-nine migrants disembarked in Malta yesterday after spending more than two weeks stranded on board rescue ships, ending a stand-off in which European Union countries had refused to offer them a safe port.
The deal calls for 300 migrants to be redistributed between eight countries, including Ireland.
Minister for Justice Charlie Flanagan said five unaccompanied child migrants would be taken in from Malta as a gesture of solidarity and humanitarian assistance.
"I am pleased to announce that we will offer to welcome five unaccompanied minors to Ireland from Malta," Mr Flanagan said.
"These children have been rescued from the Mediterranean Sea in humanitarian search and rescue missions and have been through a terrible ordeal.
"They will be welcomed to Ireland under our Irish Refugee Protection Programme, which has a proven record of helping those who are most vulnerable.
"We will ensure that they are provided with all of the necessary supports".
But Italian Interior Minister Matteo Salvini has demanded a "clarification" since the agreement was announced.
"I am and remain absolutely against any new arrivals in Italy," Mr Salvini said on Twitter.
"Caving to the pressures and threats of Europe and the non-governmental organisations is a sign of weakness that Italians don't deserve."
Two vessels had been sailing back and forth in Maltese waters for days after Italy, Malta and all other EU countries refused to offer them a port of safety.