The M5-RFP movement on Friday released a strong statement against the colonels who seized power in 2020, further extending their rule after they failed to meet a March deadline to hold elections and hand over power to a civilian government.
Two sources confirmed that Boubacar Traore, who signed the statement, had been detained.
A member of his entourage said he was taken by intelligence agents from his office in the building housing the prime minister's services.
The M5 statement was widely considered to set the seal on the breakdown in relations between the colonels and the prime minister they appointed in 2021.
The statement also opposed proposals to promote the colonels to the rank of generals and to launch talks with armed jihadists.
The proposals emerged from recent national consultations organised by the junta which intends to carry them out.
The M5 said the proposals, which include several more years of military rule, "offended public opinion."
AFP could not confirm if Maiga, who was appointed by the junta, supported the statement from M5, which is riven by factionalism.
But Traore told AFP the statement came from the faction backing Maiga.
But the prime minister has made no comment.
There has been speculation for months that Maiga, who appears isolated with limited room to manoeuvre, is to be replaced.
The colonels have kept a tight hold on the reins of power, following a second putsch in 2021. They have not set a new date to hand over power.
Maiga had announced the junta will only organize elections once the security situation has completely stabilised.
In April, the military authorities suspended all party-political activities after muzzling opponents, journalists and human rights activists.
Mali has since 2012 been plunged into a political and security crisis fueled by attacks from jihadist and other armed groups, as well as a separatist struggle in the north.