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The arrests were orchestrated by Vice President Assimi Goita, who led last year's coup that overthrew former President Ibrahim Boubacar Keita.
'They resigned, their release was scheduled, we have nothing against them,' said Goita aide Baba Cissa.
Ndaw and Ouane's whereabouts will be kept secret to protect their security, Cissa 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.
He has promised that next year's elections will go ahead. But on Thursday his legal advisor Youssouf Coulibaly suggested this commitment was not set in stone.