The country, formally the main part of the Ottoman Empire, has always denied the deaths during World War One 100 years ago were genocide.
Instead Turkey says most of those killed were involved in fighting during the war.
Armenia claims up to 1.5 million of their people were massacred as the Ottoman Empire broke apart from 1915 onwards.
Turkey has now summoned the Vatican ambassador to explain the Pope's remarks.
Commentators say the pontiff would have been well aware of the offence he would cause to Turkey.
During a Mass to mark the 100th anniversary of the killings Pope Francis said they were the "first genocide of the 20th century".
"In the past century our human family has lived through three massive and unprecedented tragedies," the Holy Father said.
Francis had been under pressure to use the word genocide by the Armenian Church, with which he has strong links.
During a meeting last week he avoided using the word instead saying Ottoman officials were guilty of "systematically planning the annihilation of their brothers".
The move is likely to anger Turkey.
The country responded with fury with Pope John Paul II used the word in 2000.