Mr Ouattara who is the Head of Regional Group Ecowas, disclosed that the troops would be leaving for Nigeria to tackle the ongoing Boko Haram campaign in the country.
Mr Quattara however, did not confirm the number of troops that Nigeria will leave behind in Mali. Mali would be holding its general elections on 28 July.
The Nigerian troops form part of a force of 12,600 African troops that took charge from a French-led mission early July.
A combined troops of French and West African succeeded in driving militants out of northern Mali in February.
The UN force, with its French acronym Minusma has aligned with the Malian army to secure the forthcoming election. The troop is expected to grow up to 11,200, plus 1,400 police towards the end of the year.
Speaking at a summit of West African nations in Abuja, the Nigerian capital, President Ouattara said, the withdrawal was “because of the domestic situation in Nigeria”.
“They are not withdrawing everyone. A good part of the troops are going to be there,” he said.