The army first accused the M23 insurgents of killing at least 50 civilians in Kishishe village in eastern North Kivu province, before the government put the number of dead at more than 100.
M23 rebel group must withdraw from its occupied territories in the eastern Democratic Republic of Congo or face intervention by regional forces, leaders of five African countries warn.
Congolese officials say the identity of the dead man who crossed the border was not known, but that no Congolese soldier on duty in the area had been reported missing.
US Secretary of State Antony Blinken will hold talks with Rwandan President Paul Kagame, as he faces calls from campaigners to pressure Kigali over its human rights record and alleged support of DRC rebels.
Protesters in capital Kinshasa seek expulsion of Rwandan envoy over Kigali's alleged support to notorious M23 rebels – a primarily Congolese Tutsi group.
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