"We will not allow historical incidents to be taken out of their genuine context and be used as a tool to campaign against our country," Mr Erdogan was quoted by Reuters as saying in a speech on Tuesday.
"I condemn the pope and would like to warn him not to make similar mistakes again," he added.
At a mass conducted in the Armenian Catholic service at Peter's Basilica, the pope said humanity had lived through "three massive and unprecedented tragedies" in the last century.
"The first, which is widely considered 'the first genocide of the 20th Century', struck your own Armenian people," he said.
"Concealing or denying evil is like allowing a wound to keep bleeding without bandaging it," the pope added.
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