The figure is at the bottom end of previous estimates, which had previously put the number of privately-owned guns at between five and ten million.
The new national gun register bundles together the data from some 551 local authorities, which were previously not interconnected. Some still had not even digitized their records, and still kept weapons ownership information on index cards.
According to the Interior Ministry, this will be the first time that reliable information on the legally-owned guns will be available to the police and other security authorities. A spokesman said the initiative would make an important contribution to public safety.
With the move, Germany is conforming to a European Union directive which obliges all member states to set up a weapons register by the end of 2014. But calls for centralized, easily accessible information were intensified after the 2009 school shooting in Winnenden, southwestern Germany, where 16 people were killed, including the 17-year-old perpetrator.