Ndaw and Ouane's whereabouts will be kept secret to protect their security, Cissé told Reuters. He declined to detail any plans for their replacement.
Goita ordered their arrest after a cabinet reshuffle in which two fellow coup leaders were sacked from their posts.
Their resignations coincided with a visit by an Economic Community of West African States delegation to press the military to back down. ECOWAS has floated the possibility of sanctions against the officers responsible for the takeover.
Mali's influential M5-RFP political coalition, which led antigovernment protests ahead of last year's coup, has opposed the leadership of Ndaw and Ouane, but it said it would strongly oppose Goita's appointment as president.
Though considered by analysts to be Goita's most likely future governing partner, the coalition said talks with ECOWAS had failed in part because of him.
ECOWAS did not comment about the talks on Thursday.
“The discussions yesterday were unsuccessful because Assimi wants to be the president, which is contrary to the texts of the Transition Charter,” Nouhoum Togo, a spokesperson for M5-RFP, told Reuters.
“Nowhere is it stipulated that the vice-president can replace the president,” he said.