The hearing began in the early afternoon in a court at a military camp in Goma, the capital of North Kivu province, where the massacre occurred.
Congolese soldiers had last Wednesday stopped a religious sect from holding a demonstration against United Nations peacekeepers in the city.
An internal army document seen by AFP and verified by security officials, gave a death toll of 48 civilians -- 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.
Military prosecutor Colonel Michel Kachil told the courtroom on Tuesday, however, that 56 people had been killed in the crackdown.
Six soldiers -- including two officers of the elite Republican Guard -- stand charged with crimes against humanity and of violating orders.
Colonel Mike Mikombe, one the accused Republican Guard officers, denied the charges before the tribunal. The other defendants were not called upon to speak.
The launch of proceedings comes after the DRC's interior and defence ministers travelled to Goma over the weekend to investigate the incident.
After announcing the arrest of the two Republican Guard officers, Interior Minister Peter Kazadi also stated on Monday that North Kivu's military governor, General Constant Ndima, had been recalled to the capital Kinshasa for "consultations".
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, known as MONUSCO, 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.
In New York on Tuesday, Farhan Haq, the deputy spokesman for the UN secretary-general, said that MONUSCO "strongly encourages a thorough and independent investigation" into the killing of protesters in Goma last week.
The trial of the six accused soldiers is due to continue on Wednesday.
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