Lieutenant-colonel Emmanuel Zoungrana, 42, was provisionally allowed to return home in the capital Ouagadougou on Tuesday by a military tribunal, a relative told AFP, asking not to be named.
"My husband has just been abducted," Aminata Diarra posted on social media.
Zoungrana had first been detained on January 14, 2022, when Burkina was still under a civilian government with Roch Marc Christian Kabore as president.
The lieutenant-colonel, who had led the 12th commando infantry regiment in the north, was granted a provisional release on December 15 the same year.
Burkina Faso then went through two coups, the second of which brought acting president Captain Ibrahim Traore to power.
Zoungrana was detained again for "attempted destabilisation of State institutions", this time against Traore's regime.
The officer's lawyer said he was moved from jail for health reasons in December 2023 but still kept under watch.
Jihadist rebels affiliated with Al-Qaeda and the Islamic State group have waged a grinding insurgency since 2015 that has killed thousands and displaced millions.
Zoungrana was decorated for re-capturing localities from armed jihadists.
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