At least 9,000 Rohingya died in Myanmar, also known as Burma, between 25 August and 24 September.
"In the most conservative estimations" at least 6,700 of those deaths have been caused by violence, including at least 730 children under the age of five, according to Medecins Sans Frontieres
The number is much higher than Myanmar's official figure of 400.
More than 647,000 Rohingya have fled into Bangladesh since August, MSF says.
"What we uncovered was staggering, both in terms of the numbers of people who reported a family member died as a result of violence, and the horrific ways in which they said they were killed or severely injured," MSF Medical Director Sidney Wong said. "The numbers of deaths are likely to be an underestimation as we have not surveyed all refugee settlements in Bangladesh and because the surveys don't account for the families who never made it out of Myanmar," Mr Wong said.
According to MSF:
69% of the violence-related deaths were caused by gunshots
9% were due to being burnt to death in their houses
5% were beaten to death.
Among the dead children below the age of five, MSF says more than 59% were reportedly shot, 15% burnt to death, 7% beaten to death and 2% killed by landmine blasts.