German Foreign Minister Annalena Baerbock speaks with the media as she arrives for a meeting of NATO foreign ministers at NATO headquarters in Brussels, Thursday, April 7, 2022. AP
Baerbock will meet junta leader Assimi Goita and Foreign Minister Abdoulaye Diop, the spokesman said.
She will then continue to Niger for talks with President Mohamed Bazoum and Foreign Minister Ibrahim Yacoubou and return to Germany on Saturday.
Baerbock's aim is to "get a precise picture of the political and security situation on the ground" as Germany weighs its ongoing participation in military missions in Mali, the spokesman said.
"The Bamako government has lost the confidence of the international community in recent months, notably by holding back democratic transition and by intensifying military cooperation with Moscow," Baerbock said in a statement before her departure.
"In this context, we shall have to question a new German commitment in the Sahel region," she added.
Baerbock's visit to Niger is to a country with a key role regarding the redeployment of international forces in the Sahel.
But her tour began on a day that saw the EU decide to halt its military training missions in Mali while maintaining a presence in the Sahel, which EU foreign policy chief Josep Borrell insisted "remains a priority".
Borrell said developments in Mali "have forced us to see there were not sufficient guarantees... on non-interference by the Wagner group", a Russian private military organisation that France and other countries say is operating in Mali as an armed force.
Russia says it has only supplied military instructors to Mali but the EU is concerned about reports that the group joined Malian soldiers in an operation last month in the village of Moura in which more than 200 civilians were killed.
German Defence Minister Christine Lambrecht visited German troops stationed in Mali at the weekend and spoke of "atrocities" in Moura.
Mali's military-dominated government says it "neutralised" 203 jihadists there, but witnesses interviewed by media and Human Rights Watch (HRW) say soldiers actually killed scores of civilians.
Germany has around 1,100 soldiers deployed as part of the 14,000-strong United Nations peacekeeping mission in Mali, known as MINUSMA.
The EU state has also contributed some 300 troops to the EU military training mission (EUTM Mali) in the Sahel country.
Germany's parliament is due to decide whether to extend the country's participation in MINUSMA and EUTM Mali in May.
Former colonial power France announced in February it was pulling thousands of troops out of Mali, plunging the future of Germany's military engagement into doubt.
Mali has been struggling to contain a brutal jihadist insurgency that first emerged in 2012, before spreading to neighbouring Burkina Faso and Niger.
Thousands of soldiers and civilians have been killed and two million people forced to flee their homes by the Sahel-wide conflict, of which Mali remains the epicentre.
France announced its military pullout due to a dispute with Mali's military junta, which seized power in 2020 and has since defied international calls to swiftly restore civilian rule.