Three suspected members of Palestinian militant group Hamas were arrested in Berlin on Wednesday for allegedly planning attacks on Jewish and Israeli sites, German prosecutors said, with weapons and ammunition also seized.

The male suspects were "foreign operatives" of Hamas, who have "have been involved in procuring firearms and ammunition for the organisation" in Germany, said federal prosecutors in a statement.

But Hamas denied any connection to the three men.

According to German prosecutors, an AK-47 assault rifle and several pistols, along with a stash of ammunition, were seized when the suspects were arrested.

"The weapons were to be used by Hamas for deadly attacks targeting Israeli or Jewish institutions in Germany," added the statement.

According to news outlet Der Spiegel, searches were also carried out in the eastern city of Leipzig around the same time as the arrests in Berlin.

Interior Minister Alexander Dobrindt hailed law enforcement officials for "averting a terrorist threat."

A suspect with Hamas connections had entered Germany several months ago and had been under observation since, Dobrindt told reporters in Brussels.

"We are clearly a target for terrorists, which is why we must always be well prepared to defend ourselves against them," he added.

But in a statement, Hamas said it has "no connection with the individuals arrested today in Germany," adding the allegations that the detainees had links to the Islamist group were "completely unfounded."

The suspects will appear in court on Thursday. (AFP)