Militants disguised as UN peacekeepers – in distinctive blue helmets and driving a vehicle marked with the UN logo – struck two bases near the airport in Timbuktu.
The UN mission confirmed one of its peacekeepers had been killed.
More than a dozen others, including many French soldiers, were wounded, according to the government.
In a statement, the security ministry said the attack involved dozens of rockets fired by militants “wearing blue helmets”. Two vehicles were also packed with explosives.
One of the vehicles exploded, the ministry said, while the other, bearing the UN symbol, was stopped.
The ministry said that while five people were seriously injured, the fighting had ended and the situation was under control.
Attacks against UN peacekeepers and government forces are common in Mali, a former French colony which also has a French military presence.
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But one foreign security source told the AFP news agency the scale of the most recent assault was “unprecedented” in Timbuktu.
“We’ve never seen an attack like this,” a separate official from the Timbuktu governorate said.
The UN mission has been deployed in Mali since a 2013 Tuareg separatist uprising. It has more than 11,000 troops and 1,741 police, and is considered one of the UN’s most dangerous missions.
Before Saturday’s rocket and car bomb attack, 162 UN personnel had been killed in the five years since the mission began.
Seven peacekeepers have been killed this year.