President Recep Tayyip Erdogan’s comments came during a joint press conference Saturday with Djibouti’s President Ismail Omar Guelleh.
"There are serious games being played with the Islamic world and one of them is Islamophobia," said Erdogan.
Another was the "clash of civilizations," he said.
He gave as proof "the hundreds and thousands" of deaths in Iraq, deaths in Afghanistan and Pakistan, Syria and Egypt.
"It doesn’t matter what faith a terrorist is, a terrorist is a murderer," added Erdogan. "If he is a Muslim he is still a killer, if Christian still a killer or if he is a Jew then he is still a killer."
"Because, after all, innocent people are dying," he said.
Meanwhile, Erdogan said Turkey was engaging Europe to see if it could tolerate a Muslim-populated country, referring to its EU membership bid.
"There is a theory that 'the European Union is a Christian entity,'" said Erdogan, adding that should Turkey be accepted in the EU, that theory would have to go.
"Turkey is in NATO, Turkey is in the OECD (Organisation for Economic Co-operation and Development), Turkey is a member of many organizations," he said. "Why aren’t you accepting Turkey into the European Union? This means there is a different problem."
Erdogan added that Turkey was now a powerful country that will not "beg to come to your doors." "If accepted, it will enter the EU, if not, it will draw its own path," he said.
- Somali bomb attack
Concerning Thursday's bomb attack near a hotel accommodating a Turkish delegation in Mogadishu, Erdogan said he did not believe it was targeting Turkey.
"I do not want to think it could be so," he said.
Erdogan will visit Somalia Sunday.
- Visit in Djibouti’s National Assembly
President Erdogan also spoke at the country's National Assembly, where he said that Turkey would provide scholarships for 3,500 African students studying in Turkey.
He stated that there were currently 65 students from Djibouti studying in Turkey and that he wished to raise the number to 100.
He also commented on the situation of the two countries on the two different continents, saying: "Although both countries are models of stability, the instability of the region, the conflicts and terrorism affect them directly."