Junta leader Assimi Goita replaced the deputy general chief of staff, the head of military security and the ground forces' chief of staff, the document said.
A senior officer who asked not to be named told AFP that the three were fired during an emergency defence council meeting on Tuesday "for poor results" on the battlefield.
"Their firing is linked to bad results by troops on the ground and failures of intelligence in anticipating and countering attacks," the officer said, adding that some of the three would be prosecuted.
Since 2012 Mali has been locked in a security crisis fuelled by violence from jihadists linked to Al-Qaeda and the Islamic State group.
The junta took over through coups in 2020 and 2021 and has since struggled to stem the attacks.
Al-Qaeda-linked fighters have recently appeared to be seeking to isolate the capital Bamako by increasing operations on the surrounding roads.
Since September they have blockaded fuel imports from neighbouring countries, disrupting daily life in the landlocked country.
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