"Security in the Sahel region is in Germany's particular interest," Pistorius said in a statement ahead of the trip to Niger and Mali.
"Although we are ending our military involvement in (the UN mission in Mali), we remain committed to the region," he said.
The UN mission in Mali, MINUSMA, was created in 2013 to help stabilise the country as it battled a jihadist insurgency.
Germany announced last year that it will withdraw its troops from the mission by May 2024.
The decision came after the German army, known as the Bundeswehr, had repeatedly run into operational problems with the ruling junta.
There had also been growing tensions between the UN mission and Mali's military rulers following the alleged arrival of Wagner operatives from Russia to bolster government forces.
However, the German cabinet last month agreed for up to 60 German soldiers to participate in the new EU-led military mission EUMPM, based in Niger.
Speaking at an air transport hub in Niamey on Wednesday, Pistorius said both military and development support were vital "to stabilise the region further and even better than in the past".
The airbase will be "of particular importance... when we withdraw from Mali, because we will have the focus here after the withdrawal from Mali," Pistorius said.
Pistorius, who was appointed defence minister in January, is also being accompanied on his trip by Development Minister Svenja Schulze.
"We are here together because we also want to show that security means more than just military security," she said at the airbase.
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