On Saturday, the Congolese army said Captain Patrick Rutasura Gasore had died on Thursday evening in the city of Goma, without giving further details.
The army added that it had launched an investigation into the circumstances surrounding his death and arrested two suspects.
However, several sources said residents of the captain's neighbourhood in Goma had lynched him after mistaking him for an M23 fighter.
The Tutsi-led M23, which is allegedly backed by Rwanda, has captured swathes of territory in eastern Democratic Republic of Congo since launching an offensive in late 2021.
A period of several months of calm was broken last month when fighting erupted again between the M23 on one side, and Congolese soldiers and pro-state militias on the other.
Two people told AFP that on Thursday evening, residents of Captain Gasore's neighbourhood began to hurl stones at him after he left his house.
"They were saying he was an M23," said one of the residents, who added that the captain later died.
Erick Sematungo Rutegeranya, a relative of Gasore's, called for "justice" against those who had killed the military man.
Gasore was a member of the Banyamulenge, a Congolese Tutsi community from South Kivu province.
Militias have plagued eastern DRC for decades, a legacy of regional wars that flared in the 1990s and 2000s.
Several Western countries, including the United States and France have concluded that Rwanda backs the M23. Kigali denies the claim.
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