The foreign ministry reportedly told the envoy it was “disappointed” by the comments, which caused a “problem of trust” between Turkey and the Vatican.
Armenia and many historians say up to 1.5 million people were systematically killed by Ottoman forces in 1915.
Turkey has consistently denied that the killings were genocide. report BBC
The Pope’s comments came at a service in Rome to honour a 10th Century mystic, attended by Armenia’s president.
The dispute has continued to sour relations between Armenia and Turkey.
The Pope first used the word genocide for the killings two years ago, prompting a fierce protest from Turkey.
At Sunday’s Mass in the Armenian Catholic rite at Peter’s Basilica, he said that 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, in a form of words used by a declaration by Pope John Paul II in 2001.
Pope Francis also referred to the crimes “perpetrated by Nazism and Stalinism” and said other genocides had followed in Cambodia, Rwanda, Burundi and Bosnia.
He said it was his duty to honour the memories of those who were killed.
“Concealing or denying evil is like allowing a wound to keep bleeding without bandaging it,” the Pope added.
On Sunday, Pope Francis also honoured the 10th Century mystic St Gregory of Narek by declaring him a doctor of the church. Only 35 other people have been given the title, including St Augustine and the Venerable Bede.
Armenia marks the date of 24 April 1915 as the start of the mass killings. The country has long campaigned for greater recognition of what it regards as a genocide.
Analysis: David Willey, BBC News, Rome
The Pope was perfectly conscious that by using the word “genocide” he would offend Turkey, which considers the number of deaths of Armenians during the extinction of the Ottoman Empire exaggerated, and continues to deny the extent of the massacre.
But the Pope’s powerful phrase “concealing or denying evil is like allowing a wound to bleed without bandaging it” extended his condemnation to all other, more recent, mass killings.
Pope Francis’ focus today on Armenia, the first country to adopt Christianity as its state religion, even before the conversion of the Roman Emperor Constantine, serves as yet another reminder of the Catholic Church’s widely spread roots in Eastern Europe and the Middle East. More than 20 local Eastern Catholic Churches, including that of Armenia, remain in communion with Rome.