Nurettin Canikli, Turkey's deputy prime minister, said the pontiff's comments regarding the massacre - which started in 1915 - were "greatly unfortunate."
The pontiff wrapped up a three-day visit of Armenia on Sunday by holding an open-air liturgy at the seat of the nation's Oriental Orthodox church, the Armenian Apostolic Cathedral in Etchmiadzin.
During a prayer meeting with the Pope on Saturday night, patriarch, Catholicos Karekin II spoke about a need for justice regarding the 1915 killings and for Turkey the acknowledge it's past.
Pope Francis instead highlighted the need for reconciliation, highlight differing opinions between the two leaders.
The pontiff was also due to visit Orthodox's border with Turkey, which Turkey has closed in opposition of claims local ethnic Armenians have been controling the Azerbaijan region of Nagorno-Karabakh.
Pope Francis is also expected to release a dove near the border at the Khor Virap monastery which lies near Mount Ararat where - according to the Bible - Noah's Ark landed after the flood.
The Catholic leader expressed a desire to see the Armenia-Turkey border reopened.