The wave of mass arrests that followed the attempted coup d'etat raises concerns about the status of free speech in Turkey, the German chancellor told the Turkish president on Thursday.
Germany and other European Union countries have expressed concern that Erdogan is undermining the rule of law and freedom of expression in Turkey with a massive, long-running crackdown following last year's failed coup attempt against the government.
"This is why it is important, in the decisive phase, that the freedom of expression of opinions be supported and, in relation to this, we talked about the freedom of the media", said Merkel.
Ataturk remains a revered figure in Turkey and his image remains ever present in the country but he would not have seen eye to eye with Erdogan on many issues.More news: Syria: UN, de Mistura, Geneva talks postponed till February 20
Merkel said efforts must be made to ensure the separation of powers and the diversity of society during this "deep political transformation".
He said Berlin was also sheltering members of what Ankara calls the "Gulenist Terrorist Organisation" (FETO), the network of USA -based cleric Fethullah Gulen, which Ankara blames for last July's coup bid.
Erdogan rebuked Merkel for using the expression "Islamist terrorism", saying the phrase was not correct and saddened Muslims.
'We agree we want to cooperate, we are all affected by this.More news: 2016 shows sales drop for Harley-Davidson by 3.9%
"The term "Islamist terror" severely upsets us Muslims".
Merkel's visit to Ankara on Thursday comes as ties between Turkey and Germany are strained.
'Such an expression is not correct because Islam and terror can not be associated.
"As a Muslim president personally I can not accept that".More news: Reversal on Green-Card Holders Highlights Casual Cruelty of Trump's Immigration Order
New President Donald Trump has not shied away from using the term, speaking of "radical Islamic terror" during the election campaign and condemning Obama for not using the term. About 1.4 million refugees came to Germany since 2015.