Turkey's Directorate of Religious Affairs, Mehmet Görmez, on Monday described comments by Pope Francis that the 1915 mass killing of Armenians was genocide as immoral and said the Vatican should look to its own history before levelling accusations of casting stones.

Francis this month became the first head of the Roman Catholic church to publicly call the killing of as many as 1.5 million Armenians "genocide", prompting a row with Turkey, which summoned the Vatican's envoy and recalled its own.

"The Vatican will come out as the biggest loser if we are all giving account for past sufferings and pain caused," Mehmet Görmez told Reuters in an interview.

"Is the current situation of millions of Syrian refugees much less cause for concern to the Vatican than what happened during the Armenian deportation?" he said, referring to refugees from Syria's civil war being sheltered in Turkey.

"I find the Pope's statement immoral, and can't reconcile it with basic Christian values."

Görmez said Europe's weak economy and its difficulties integrating immigrants were the root causes of rising Islamophobia on the continent.

"Islamophobia should be considered a crime against humanity, just like anti-Semitism," he said.

Görmez also said violence carried out by groups such as the self-proclaimed Islamic State of Iraq and al-Sham (ISIS), Boko Haram, Al Shabaab and al Qaeda was a consequence of ignorance and poverty, as well as of the exploitation of the Middle East and Africa for two centuries.

He called on Islamic scholars and clerics to be self-critical about how they were raising new generations.

"Islam was a religion creating civilisation throughout history. When educating Muslim children, clerics should reflect on the comparison between that and today's Koranic interpretations that incite violence," he said.