The federal prosecutor’s office said in a statement on Wednesday that, during the course of the arrests, “various weapons, including an AK 47 assault rifle and several pistols, and a significant amount of ammunition, were found”.
It added: “The weapons were intended for use by Hamas in assassination attacks on Israeli or Jewish institutions in Germany.”
Prosecutors in Germany typically only refer to suspects by their first name and an initial.
German media report the men were arrested when they met for a weapons handover in the capital.
Police searches also took place in the cities of Leipzig and Oberhausen around the time of the Berlin arrests, according to newspaper Der Spiegel.
The three have been charged with preparing a serious act of violence endangering the German state and membership of a foreign terrorist organisation.
The suspects will appear before a federal judge on Thursday, the federal prosecutor said.
Hamas said in a statement that the allegations against it were “baseless” and aimed to “undermine the German people’s sympathy for the Palestinian people”.
The group added that it had a policy of limiting its activities to what it considers Palestinian territory.
The arrests come after four Hamas members went on trial in Berlin in February, accused of plotting attacks on Jewish sites in Europe.
