Mr Keïta, 75, flew to the United Arab Emirates (UAE) on Saturday for medical treatment after suffering a minor stroke, military officials said.
The junta is currently in talks with opposition and civil society groups about a transition to civilian rule.
It says it will step down in two years, but West African leaders want a quicker transfer of power.
Mr Keïta was overthrown on 18 August following mass protests against his rule over corruption, the mismanagement of the economy and a dispute over legislative elections.
The coup sparked international condemnation, but it was welcomed by many Malians.
Mr Keïta was detained by the military, but later freed.
On Thursday, he left a hospital in the capital, Bamako, after a two-day stay during which he was treated for a minor stroke, AFP news agency reported.
His former chief of staff said he could be away for up to15 days.
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