The move came after several dozen members of the Nyatura militia -- one of scores that operate in the region -- surrendered to government forces last week.
President Felix Tshisekedi placed North Kivu and neighbouring Ituri province under a "state of siege" on May 6 in a bid to clamp down on the militia groups.
Civilian governors have been replaced by senior army and police officers under the measure.
Jean-Marie Bonane, a self-styled "general" and head of the Nyatura militia, said the soldiers were freed as "a peace gesture".
The militia claims to defend the interests of ethnic Hutus in North Kivu, but is accused of backing the Democratic Forces for the Liberation of Rwanda (FDLR), a notorious Rwandan Hutu group.
An estimated 120 militia groups operate in the mineral-rich eastern DRC, many of them a legacy of two regional wars from 1996 to 2003.
The conflict has claimed hundreds of civilian lives this year alone.
Also Friday, the army said two Congolese soldiers were killed in an ambush in neighbouring South Kivu province in the Fizi area.
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