The pope has stirred Turkish anger during a three-day visit to ex-Soviet Armenia by using the term for the century-old slaughter that Ankara furiously rejects.
Turkish Deputy Prime Minister Nurettin Canlikli labelled the pope's declaration "very unfortunate" and said it bore traces of "the mentality of the Crusades."
"It is not an objective statement that conforms with reality," Canlikli said.
The Vatican rejected the allegations and said the pontiff was trying to build "bridges not walls" and had nothing against Turkey.
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"Francis prayed for reconciliation of all and did not say one word against the Turkish people. The pope does not conduct Crusades, is not looking to organise a wars."
When Francis first used the term "genocide" in 2015, on the centenary of the 1915-1917 killings that Armenians say wiped out some 1.5 million of their people, Ankara angrily recalled its envoy from the Holy See for nearly a year.
Armenians have long sought international recognition for the World War I killings as genocide.
The pope yesterday visited the Armenian genocide memorial in Yerevan but sought to strike a conciliatory tone during evening prayers.
"May God bless your future and grant that the people of Armenia and Turkey take up again the path of reconciliation, and may peace also spring forth in Nagorny Karabakh," he said.
Later today Pope Francis is set to round off his visit to Armenia with a symbolic visit to pray at the Khor Varap Monastery on the border with Turkey.
"We should follow God's call and hasten the steps towards ... The communion between us becoming full," Francis said, insisting such unity "does not mean a submission of one to the other or an absorption."
The Armenian Apostolic Church separated from the Catholic Church in the fourth century after rejecting Roman Catholic and Eastern Orthodox doctrine of Jesus Christ's dual nature - instead professing that Christ is both divine and human simultaneously.
According to the 2011 census, some 96 per cent of the country's population of some three million belong to the Armenian Apostolic Church.