The former senator cited his role at a law firm where a senior partner was tapped to represent the president in the Russia probes.
The president alluded to the Holocaust, saying the United States "will not allow the horror and atrocities of the last century to be repeated."
The administration did add sanctions on Iran for its ballistic missile testing.
President Trump gets flak for not moving the embassy to Jerusalem and for some of his appointments.
It is not known who initiated the call, which reportedly lasted 20 minutes and only dealt with details pertaining to the U.S. president's visit next week to Israel.
The cosmetics heir and the casino magnate differ on the best way to bring peace, presenting a conundrum to the president.
Comey was speaking to the Anti-Defamation League, which has long sought uniform standards for hate crimes data across the United States and in Europe.
The next president has not assured his Jewish supporters on Israel or the fight against Muslim extremism.
Erdogan chided the international community for its silence and also called on Turks to make more visits to the Al-Aqsa mosque to protect its Muslim identity.
A range of Jewish groups has urged the president to protect the ban on politicking from the pulpit.