"There will either be a civil war or another scenario... his assassination", Defarges had said on Saturday, predicting what he termed a "catastrophe" through polarization in Turkey, given strengthened powers for Erdogan narrowly endorsed in Turkey's referendum on April 16 versus widespread Turkish disquiet.
The "Yes" camp won just over 51 percent in the vote, a narrower-than-expected victory, but Turkey's top election board last week rejected opposition calls to annul the referendum after complaints of vote-rigging.
Earlier on Monday Erdogan filed a complaint against Defarges, and Ankara prosecutors launched a probe, according to presidential and judicial sources, who asked not to be named due to restrictions on speaking to the media.
If found to be in good mental health, his alleged links with the outlawed Kurdistan Workers' Party (PKK) or US-based Muslim cleric Fethullah Gulen - blamed by Ankara for orchestrating the failed coup - should be investigated, Aydin said. "For it is an effort to lay additional groundwork for something else", Ibrahim Kalin told a press conference at the presidential complex in the capital Ankara.
He said Defarges's comments would have "legal consequences" and the researcher had to face them.
Defarges, a senior fellow at the French Institute of International Relations, has apologized through Twitter, saying some of his words were "clumsy" and "misinterpreted".
"In light of the terrorist groups which have been hosted by many European countries and all the incidents urging assassination of our president that took place there, it is clear that the suspect's remarks are far from a simple opinion, but are in fact an incitement", Erdogan's lawyer said. "@IFRI_ should terminate his fellowship, apologise", Gulnur Aybet tweeted.
Mr Defarges on Sunday offered "sincere apologies" for his remarks.
Europe's reactions in the wake of the Turkish public's recent approval of constitutional changes show an "eclipse of reason", the president's spokesman said Monday. It was a test to see how Europe would react, he added.
The same critics also accuse Mr Erdogan of becoming increasingly authoritarian after 14 years in power - first as prime minister and then as president.
There have been a number of prosecutions for insulting Erdogan, with artists, journalists and schoolchildren all targeted.