Around 1,000 people had been protesting outside the local airport and a military camp housing the UN peacekeeping force, known as MINUSMA, in Sevare, near the central city of Mopti.
Protesters set fire to tires on Saturday before ransacking UN containers outside the camp.
"The protesters stole logistical and construction equipment," the UN mission said. "Camp security was not impacted, but these acts of vandalism are totally unacceptable."
The fragile Sahel country hosts France's military mission in the Sahel and UN peacekeeping troops as well as contingents from a five-nation anti-jihadist group.
Northern Mali fell into the hands of jihadists in 2012 before the militants were forced out by a French-led military intervention.
But much of the region remains unstable and jihadist-led violence has spread to the centre of the country, often sparking ethnic tensions.
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