Congolese soldiers last Wednesday stopped a religious sect from holding a demonstration against United Nations peacekeepers in the city of Goma.
An internal army document consulted by AFP, and verified by security officials, gave a death toll of 48 civilians killed -- in addition to a policemen slain by the protesters.
The Democratic Republic of Congo's government said the day after the incident that 43 people had been killed and 56 wounded.
Early on Monday, Congolese Interior Minister Peter Kazadi announced that a commander of a Republican Guard brigade as well as a regiment commander had been arrested.
A trial will be organised soon "to establish who was responsible", he told reporters in Goma.
Kazadi travelled to the eastern city in the aftermath of the crackdown to investigate the incident, alongside the Congolese defence minister Jean-Pierre Bemba.
"We interviewed all the military security officials in the city," Kazadi said. "Some military officials were immediately referred to the military prosecutor's office."
"We are asking the population to remain calm, to trust the government and our justice system, which will soon reach a verdict," the interior minister added.
The DRC's communications ministry said on Monday that the arrested officers were Colonel Mike Mikombe and Lieutenant-Colonel Donatien Bawili, both of the elite Republican Guard.
Pro-democracy group LUCHA welcomed the arrests but also called for the detention of Goma's mayor, the military governor of North Kivu province -- of which Goma is the capital -- and rank-and-file soldiers implicated in the incident.
Militias have wreaked havoc in eastern DRC for three decades, a legacy of regional wars that flared in the 1990s and 2000s.
The UN peacekeeping mission in the region is one of the largest and costliest in the world, with an annual budget of about $1 billion (915,000,000 euros).
But the UN comes in for sharp criticism in the central African nation, where many people perceive the peacekeepers as failing to prevent conflict.
Last year, dozens of people were killed in anti-UN protests across eastern DRC.
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