For many Germans, the base is synonymous with a 2009 NATO airstrike ordered by German forces that killed 91 Afghans and wounded 11, most of them civilians.
De Maiziere made an indirect reference to the incident, which caused a political furor and the resignation of several senior German officials at the time.
"Kunduz was also the place where grave decisions were made, had to be made," he said. "It is a place where there were many deaths on all sides. Let us today remember all of these deaths together."
Germany, the third-largest international troop contributor in Afghanistan after the United States and Britain, plans to reduce its force levels in the country from 4,000 to about 800 by 2015. Those remaining will be stationed in the northern city of Mazar-i-Sharif, responsible largely for training and support of Afghan troops.
The U.S. is expected to keep about 10,000 troops in Afghanistan as a residual force after 2014, but no final decision has been made.