Six people were killed on Friday when mutinous soldiers firing their weapons into the air stormed through the streets of the capital Conakry and other cities, demanding the dismissal of senior commanders and a pay rise.
Conte, himself a soldier, who has ruled Guinea for 23 years after a military coup, on Friday agreed to meet the soldiers who have been striking over pay and conditions.
They are demanding unpaid salaries totalling 300 million Guinean francs ($100,000) and are angry at lack of promotions.
They also want compensation for victims of peacekeeping missions undertaken years ago in neighbouring Sierra Leone, Liberia and Guinea-Bissau.
The army alleges that the authorities have been holding back wages since 1996, the year when a mutiny claimed the lives of 300 soldiers.