The army were targeted on a military post in the Menaka region close to the border with Niger, according to the government.
At least 53 soldiers and one civilian are understood to have died.
The Malian military had initially believed the death toll to be much lower.
Soldiers have been struggling to contain an insurgency of jihadist groups that is spreading from the north of the country towards its centre.
The attack is expected to raise tensions in the capital of Bamako, where protests have already taken place in the streets.
Military families say soldiers are not being properly protected, and do not have adequate resources to face the armed groups in the vast desert landscape.
This latest attack comes one month after 41 soldiers were killed during two attacks on the Malian army as they took part in a regional counter-terrorism force.
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