Her talks with leaders of all three countries are to focus on migration issues and the battle against terrorism.
Merkel, who is set to visit Niger and Ethiopia later this week, refused to acknowledge whether Germany would provide more helicopters for the MINUSMA mission.
German Chancellor Angela Merkel is making a three-nation visit to Africa next week, with the migrant crisis leading the agenda.
The Malian army is still largely absent from Mali's desert north despite a peace agreement signed past year that aimed to speed its return, placing great pressure on MINUSMA forces to keep roaming militias and Islamist militants at bay.
Extremists who took hold of the north in 2012 were pushed out by French-led forces in 2013, but targeted attacks against peacekeepers and Malian security forces continue.
Iraq may attack Turkey if they intervene in Mosul liberation
Some Iraqi officials stressed the importance of Turkey's withdrawal from any military operations on the Iraqi territories. He said that Iraq was too "fragmented" and that no one had the right to object to Ankara's presence in the north.
"The Mediterranean has become an open air cemetery, a situation we are not indifferent to", said Keita, Mali's president.
Merkel blamed Africa as being "the central problem" for the migrant crisis and pledged to do more in the fight against drug and people smuggling from Mali during the first day of her whistle-stop tour of Africa. "We will find an appropriate solution for a framework with the cooperation of Germany".
Merkel has also said that she wants the European Union and North African countries to do deals modelled on a controversial agreement with Turkey to curb migrant flows to Europe. She will visit Ethiopia on Tuesday.
"But we should be interested in whether 11 million people will have a livelihood or not", she said.
German Chancellor Angela Merkel, left, looks at Malian President Ibrahim Boubacar Keita, during a press briefing after her arrival at Bamako, Mali, Sunday, Oct. 9, 2016.