The Union Action Unit (UAS), which brings together the country's main unions, demanded "the release of all those arrested and forcibly conscripted" as army auxiliaries.
In a statement seen by AFP, the UAS described the "degrading treatment" meted out to a young man with partially impaired vision, who had been forced to enlist after he was accused of disclosing information that led to an attack.
The federation said photographs and video footage had been published of the man, clad in army fatigues and "apologizing to the president" of the junta.
Their move comes a week after the ruling military junta declared a "general mobilization" to give the state "all necessary means" to combat a string of jihadist attacks since the start of this year.
Captain Ibrahim Traore, Burkina's transitional president who staged a September coup last year, has set a goal of recapturing the 40 percent of the country's territory controlled by jihadists.
Traore's one-year general mobilization permits the conscription of all men over 18 to fight jihadist movements as one of the world's poorest countries battles an insurgency which began in 2015.
But the UAS accused the coup authorities of abusing their power, and urged "the freeing of all people detained and forcibly enrolled" after voicing criticism of the junta.
The federation said those affected should have recourse to legal redress.
Last month, human rights movements in Burkina Faso decried what they termed "systematic" attempts to limit freedom of expression and rights by the junta.