The two spoke according to Netanyahu's office on Sunday evening, when the Israeli leader called Merz to congratulate him on the election victory.
Merz's party, the Christian Democratic CDU, has confirmed the phone call but declined to comment on what they talked about.
The International Criminal Court ICC's arrest warrant against Netanyahu means that countries that have signed the court's founding document, including Germany, are obligated to arrest him if he sets foot in any of them.
Netanyahu is accused, like the former Israeli Defense Minister Yoav Gallant, of war crimes in Gaza.