Ouattara ordered senior military commanders to urge militia leaders, including former coup-plotter Ibrahim Coulibally, who is holed up in a neighbourhood of the main city Abidjan, to disarm.
"I instruct you to ask militia leaders, ask commander Ibrahim Coulibaly, to come to you and lay down arms. This should be done immediately," said Ouattara, who took power after Gbagbo's ouster on April 11.
"Nobody should illegally carry weapons," he added, warning that failure to heed this meant "they should be disarmed by force."
Coulibaly has taken position in Abidjan's northern Abobo district, while pockets of hardcore pro-Gbagbo militia are holed up in the city's northwestern Yopougon district where the new government forces tried unsuccessfully to dislodge them Wednesday.
"We will not accept pockets of belligerents to disrupt Ivorians' peace. The war is over in Ivory Coast. The country is unified, the army should be unified," added Ouattara.
Ouattara also ordered the top army officials to immediately have all soldiers return to their bases across the country.