Police received a call soon after 9pm on Thursday and officers arrived at the scene to find several people seriously injured and some dead.
"Then they heard a shot from above, they went upstairs and found one further person," said a police spokesman on Friday..
The Bild newspaper reported that eight people were wounded at the Kingdom Hall of Jehovah's Witness in the northern city that is home to Germany's biggest port.
Television footage showed dozens of police cars as well as fire engines blocking off streets and some people, wrapped in blankets, being led by emergency service workers into a bus.
"We heard shots," one unidentified witness told reporters.
"There were 12 continuous shots," he said.
"Then we saw how people were taken away in black bags."
The gunman was believed to be a former member of the Jehovah's Witness community, Spiegel magazine reported. He was aged between 30 and 40 and was not known to authorities as an extremist, the report said, citing unnamed sources.
"According to the current state of affairs, we assume that there is one perpetrator," police said in a message on Twitter.
"Police activities in the surrounding area are being successively discontinued. Investigations into the motives behind the crime are continuing."
Earlier, Germany's DPA news agency, citing a reporter on the scene, said residents in the city's northern Alsterdorf district had received warnings on their mobile phones of a "life threatening situation" and that streets had been sealed off.
Germany has been shaken by a number of shootings in the past few years. In February 2020, a gunman with suspected far-right links shot dead nine people, including migrants from Turkey, in the western town of Hanau before killing himself and his mother.
In October 2019, a gunman killed two people when he opened fire outside a synagogue in the eastern city of Halle on the Jewish holy day of Yom Kippur.
The mayor of Hamburg expressed shock at Thursday's bloodshed.
"I extend my deepest sympathy to the families of the victims. The forces are working at full speed to pursue the perpetrators and clarify the background," Peter Tschentscher said on Twitter.
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