The International Committee of the Red Cross lost contact with four of its staff on Saturday as they were driving back to their base in the town of Kidal.
"The best news we could get: our three colleagues in Mali are free, safe and sound," Peter Maurer said in his Twitter account.
One of the four was found on Sunday, an ICRC spokesman had earlier said. That Red Cross worker said the team had been accosted by a man on a motorcycle who demanded they follow him. It was not immediately clear why the three were then out of contact for several days.
The incident came a day after the group's local guide was arrested by soldiers from a regional anti-militant operation, the ICRC worker said, according to the spokesman.
The Kidal region is the center of a separatist movement and home to Islamist militants, some linked to al Qaeda, who have staged a series of high profile attacks in Mali and beyond in the past year.
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