An earlier army statement on the incident had said one soldier was killed and four wounded in the attack in Ber on Friday.
The death toll has risen to six, it said on Saturday, while "in their rout armed terrorist groups abandoned 24 bodies".
They also left behind AK-47 assault rifles and motorbikes, the army said.
It said the clashes in the Timbuktu region took place after an "attempted incursion and harassing fire by terrorist groups against FAMa (Malian Armed Forces) units".
The Malian troops were due to be stationed in Ber as part of a handover while the UN mission in Mali, known as MINUSMA, prepares to leave the country, the army said.
Mali's junta, in power since 2020, pushed the UN Security Council in June to withdraw MINUSMA by the end of the year.
- Tuaregs report army attack -
Also in Ber on Friday, former Tuareg rebels said their forces were attacked by the army and the Russian mercenary group Wagner.
The Coordination of Azawad Movements (CMA), which controls vast areas of the north, said in a statement to AFP on Saturday that there were "manoeuvres against its positions by the Malian armed forces accompanied by the Wagner militia".
The CMA is an alliance of Tuareg-dominated groups seeking autonomy or independence from the Malian state.
"The FAMa is determined to occupy MINUSMA's holdings at all costs, including those in areas under CMA control, in violation of all the security arrangements guaranteed to date by the UN mission and the international community", it added, referring to a 2015 peace agreement.
On Thursday, the former Tuareg rebels announced the departure of all their representatives from Bamako for "security" reasons, further widening the gap with the country's military rulers.
The CMA also criticises the military for having approved a new constitution in June, which it believes compromises the agreement.
Mali's military government has fallen out with former colonial power France and turned to Russia for political and military support.
Since 2012, Mali has been in the grip of a deep security crisis that began with an Islamist insurgency in the north, which has spread to the centre of the country as well as to neighbouring Burkina Faso and Niger.
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