"Nearly 1 million Rohingya are being subjected to genocide and are fleeing to Bangladesh," Erdogan said at an intercultural event in New York hosted by the Turkish American National Steering Committee (TASC).
"We never said it was Buddhists who killed them. This is indeed the case, but we never put it as such. Now I call on those who want to endear Buddhists to the world: What gives you the right to say 'Islamic terror?’" Erdogan said to thundering applause.
The Turkish president had similar criticism for the portrayal of the Daesh terror group as representing Islam.
"Whoever kills a soul, it is as if they have killed the entire humanity. This is among the principles of our faith," Erdogan said. "Nobody should dare associate Daesh with Islam or Muslims. It is a terrorist group," he said.
A number of hecklers tried to interrupt Erdogan's speech but were angrily shouted down by the audience as they were escorted out by security guards.
"Dear brothers and sisters," Erdogan said in response, "I have a favor to ask of you: Please do not sacrifice this beautiful gathering of ours to a few town hall terrorists."
Police arrested four members of the YPG terror group, TASC Co-Chairman Gunay Evinch told Anadolu Agency.
Evinch said TASC would take legal action against the suspects on the grounds of public disorder, trespassing and crimes against a head of state.
Erdogan concluded his trip to New York on Thursday after a bilateral meeting with U.S. President Donald Trump.
The Turkish president was in the city to attend the annual UN General Assembly meetings where he addressed world leaders earlier this week.