Local army spokesman Marc Elongo said the soldier, Lukusa Kabamba, was then "lynched" by angry residents before he could be arrested and died from his injuries.
Local civil society group coordinator Andre Byadunia had earlier said the soldier had been "locked up" and urged "the authorities to put him on trial and sentence him".
On Sunday, another soldier shot dead the bodyguard of a colonel before killing the colonel and five civilians at Bambu, in Djugu territory, the local authorities announced in Ituri province.