Human Rights watch said the DRC military has armed and fought alongside a coalition of militias implicated in abuses.
This included the FDLR, a Rwandan Hutu rebel group based in DRC which the Rwandan government views as a threat and accuses Kinshasa of supporting.
In return, Kinshasa claims Rwanda backs the M23 rebel group - a primarily DRC Tutsi militia that has captured swathes of territory this year.
Rwanda denies the claim. But a report by independent United Nations experts seen by AFP in August found that Kigali had provided direct support to the M23.
The Human Rights Watch findings come amid deep tensions between the two central African nations.
HRW researcher Thomas Fessy stated that DRC army units "are again resorting to the discredited and damaging practice of using abusive armed groups as their proxies".
"The [DRC] government should end this support, which leads to military complicity in abuses, identify officers responsible, and hold them accountable," he added.
The DRC's army has yet to respond to the Human Rights Watch report.
