A spokesman for Scholz told reporters that his office had summoned the head of the Palestinian mission in Berlin.
The chancellor's foreign and security policy adviser conveyed that Scholz expects the Palestinian president "to acknowledge the singularity of the Holocaust without any qualification", Steffen Hebestreit said.
"His gaffe casts a dark shadow over Germany's relations with the Palestinian Authority," Hebestreit said, referring to Abbas' comments. He added that Scholz has arranged a telephone call with Israeli Prime Minister Lapid in order to be able to speak directly with him about this incident as well.
Standing next to Scholz at the press conference, Abbas explicitly used the word "Holocausts" in his reply, drawing a grimace from the German chancellor. Germany has long argued the term should only be used to describe the Nazis' singular crime of killing six million Jews before and during World War II.
While Scholz had earlier rejected the Palestinian leader's description of Israel's treatment of Palestinians as "apartheid", he did not immediately rebuke Abbas for using the term "Holocaust".
Abbas said that "from 1947 until today, Israel has committed 50 massacres in 50 Palestinian villages".
"Fifty slaughters. Fifty Holocausts," he added.
During the Third Reich, the Germans and their henchmen murdered six million Jews across Europe.
Abbas appeared to walk back his comments.
In a written statement, his office said: "President Mahmoud Abbas reaffirms that the Holocaust is the most heinous crime in modern human history."
The statement stressed that "his answer was not intended to deny the singularity of the Holocaust that occurred in the last century, and condemning it in the strongest terms".
Abbas' remarks drew strong condemnation from leaders across Israel's political spectrum. Caretaker Prime Minister Yair Lapid called the comments, "not only a moral disgrace but a monstrous lie".
Dani Dayan, chairman of the Yad Vashem World Holocaust Remembrance Centre, had called Abbas' remarks about the Holocaust "appalling" and urged the German government to respond to the "inexcusable behaviour done inside the Federal Chancellery".
The remarks came a few weeks before the planned commemoration of the 50th anniversary of the Munich attack, in which Palestinian militants killed 11 members of the Israeli Olympic team. Relatives of the slain Israeli athletes said they plan to boycott the ceremony after failing to reach an agreement on bigger compensation from the German government.
Germany's leading Jewish group also sharply criticised the comment and expressed shock that Scholz did not repudiate Abbas' comment immediately.
Abbas "tramples on the memory of six million murdered Jews and damages the memory of all victims of the Holocaust", said Josef Schuster, the head of the Central Council of Jews in Germany.
"Such statements cannot be left uncommented. That a relativisation of the Holocaust, especially in Germany, at a press conference in the Federal Chancellery, goes unchallenged, I consider scandalous."
