Germany has been on high alert since December 2016, when a Tunisian asylum seeker with hijacked a truck, killed the driver and then ploughed it into a crowded market place in Berlin, killing 11 more people and injuring dozens, Reuters reported.
Police spokesman Sven Mueller said one of the two dead men had fired the shots, adding that nobody else appeared to have been hurt in the incident.
"There is no danger for people there anymore," Mueller said.
Local residents had reported the shots being fired at a construction site on Thursday morning.