It will include underground train stations and car parks but also state buildings and private properties, a ministry spokesman said.
A digital directory of all bunkers and emergency shelters will be drawn up so people can find them quickly using a planned phone app.
People will also be encouraged to create protective shelters in their homes by converting basements and garages, the spokesman told a press briefing.
He declined to give a timetable, saying it was a "big project" that would take "some time", involving the Office of Civil Protection and Disaster Assistance and other authorities.
The country of 83 million has 579 bunkers, mostly dating from World War II and the Cold War era, which can provide shelter for 480,000 people - down from about 2,000 bunkers previously, he said.
The key points of the plan were agreed at a conference of senior officials in June, and a special group is now looking into it, the spokesman said.
READ ALSO: How Germany is preparing for future threats of war
Since Russia's full-scale invasion of Ukraine in 2022, concerns have been growing about Moscow's potential to one day target other NATO members.
In October German intelligence chiefs warned that Russia will likely be capable of launching an attack on the military alliance by 2030.
German officials say the country is already facing a surge in Russian spying and sabotage activities.
Russian President Vladimir Putin last week warned the conflict in Ukraine had characteristics of a "global" war and did not rule out strikes on Western countries.
Rachel Loxton
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