Human Rights Watch has backed 50 other Congolese groups requesting the suspension of Lieutenant Colonel Innocent Zimurinda for allegedly ordering the mass killing of people in east of the central African country.
The activists said Mr Zimurinda, a former rebel incorporated into the army as part of a peace deal, has overseen or participated in massacres, summary executions, rape, recruitment of children and forced labour.
They further accused him of ordering the killings of 129 Rwandan Hutu refugees in April 2009 and commanding troops who raped women and girls and shot members of their families in 2009 and 2010.
This was at the time of a controversial military operation which was backed by the UN peacekeeping force, Monuc.
The aim was to flush out the rebels linked to the Hutu militia that carried out the 1994 genocide in Rwanda.
HRW said it had reports of summary executions and rapes under the command of Mr Zimurinda, who was not likely to take part in the latest operation, as recently as two weeks ago.
The government of Congo has been struggling to regain control over the country since a 1998-2003 war and accompanying humanitarian disaster that have killed 5.4 million people.