HRW says FDLR fighters began killing DRC civilians since January 20 this year.
Others were abducted by rebels and used as human shields, HRW said.
However, it noted that some of the fatalities were a result of fighting between the FDLR and government forces.
"The FDLR have a very ugly past, but we haven't seen this level of violence in years," said Anneke Van Woudenberg, senior researcher in the Africa division at HRW.
"We've documented many abuses by FDLR forces, but these are killings of ghastly proportions."
HRW researchers based their findings on interviews with dozens of refugees living at a displaced persons' camp near Goma, the capital of the eastern DRC province of North Kivu, housing people who had fled the violence.
Elena Uzuni told Al Jazeera that FDLR fighters had chased her family out of their home and killed her mother.
"Everything started when we saw the FDLR arrive. The FDLR were in our village, Bufandu, because they used to live their," she said.
"As soon as the FDLR saw the FARDC [government troops] they dispersed, and as soon as the soldiers passed by we started to hear shooting, the the FDLR came back and started to go after the population."
Separately, the DRC military said on Friday it had killed more than 40 FDLR fighters during an overnight raid.
Oliver Hamuli, a spokesman for the joint Rwanda-Congo military offensive, said several Hutu rebels were also wounded in the attack, that took place late on Thursday in Kashebere in the eastern DRC region of Masisi.
|Thousands of Congolese civilians have been left homeless after fleeing the violence
He confirmed that a second attack against FDLR fighters took place near Kashebere but was unable to confirm the number of casualties.
"The death toll there was high as well. The survivors threw the bodies in the river," Hamuli said.
The FDLR, some of whose leaders are suspected of having participated in the 1994 Rwandan genocide, has been blamed for fuelling years of violence and unrest in the DRC.
Many believe their presence in DRC led to the formation of a counter rebel group made up of Congolese Tutsis - which is also accused of grave human rights abuses.
DRC has long accused Rwanda of backing the Tutsi militia formerly led by rebel general Laurent Nkunda, currently under arrest, while Rwanda alleges DRC has assisted the FDLR.
Rwandan troops are expected to leave the country at the end of February when the military operation is due to be completed.