The attack, which was later claimed by Isis, left four people seriously injured, but some are questioning the actions of police.
Renate Künast, a politician from Germany's Green Party, provoked anger when she asked in a Tweet: "Why couldn't the attacker be shot to disable???? Questions!"
Police simply responded saying: "A Tweet with ???? is not appropriate at the current time".
In a later post, Künast elaborated on her stance, saying: "In police training, [the correct course of action] is to shoot to disable or taser/pepper spray... democracy means being allowed to ask."
@polizeiOBS besser ??? als !!! . Oder? Aber danke für die Reaktion.— Renate Künast (@RenateKuenast) July 18, 2016
Social media users who responded to the politician's Tweet were divided; some supported Künast, saying that it was a valid question, while others praised the police for risking their own lives in their work and potentially stopping further carnage in Würzburg.
Joachim Herrmann, interior minister for Bavaria, had praised the efforts of the police when he spoke to press on Monday night.
Herrmann said that it was "right" that the police's actions had prevented "further terrible acts". The officers opened fire on the attacker when he ran towards them.
Würzburg prosecutor Bardo Backert claimed on Tuesday that the teenager attacked police officers with his axe. He said he was “completely convinced the police were justified in shooting the attacker dead.”
Backert added that he could "in no way understand how politicians sitting in their chairs can make such comments."
On Tuesday Herrmann re-emphasized his support for the police, saying he did not have “the slightest doubt about the validity of the police operation.”
Rainer Wendt, a police spokesperson, told the Saarbrücker Zeitung: "When police officers are attacked, they're not going to use kung fu. Sometimes, unfortunately, that results in the death of the perpetrator, but that can't be helped. The actions of the police will now be investigated by the public prosecutor's office."
He criticized Künast directly, saying "We don't need parliamentary smart alecs" and that she had "no idea" of the reality officers face when dealing with this kind of scenario.
The Bavarian State Criminal Police Office has opened an internal investigation - standard procedure following the use of firearms by officers. The investigation will clarify the actions of the special commando, and decide whether the shooting was justified.