"We lost two men today at about 3am (0300 GMT) at our checkpoint north of Timbuktu," a defence ministry official said. The attack by unknown assailants was confirmed by a security source at MINUSMA, the UN mission in the country.
The ministry official said several soldiers had also been hurt in the "heavy arms" attack against the checkpoint and a Malian army vehicle hijacked.
The toll so far was "provisional", he said. "We will provide further details today on this criminal attack," he added.
Jihadist groups linked to Al-Qaeda seized control of Mali's vast arid north from March 2012 until January 2013 when they were pushed back by forces from France, the country's former colonial master.
But parts of the remote north remain out of the control of the army or of the UN military mission as the country struggles to restore peace.
There were hopes of a return to stability in May when northern-based loyalist militias signed a peace deal with Tuareg rebels in the area, but the deal remains fragile.
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