The group, known by its French acronym MSF, says the survey it conducted in refugee camps in Bangladesh estimated that at least 9,000 Rohingya died in Myanmar's Rakhine state between Aug. 25 and Sept. 24. About 630,000 Rohingya have fled Myanmar into Bangladesh to escape what the United Nations has called "ethnic cleansing."
MSF added taht the dead included at least 730 children under the age of five.
"We met and spoke with survivors of violence in Myanmar, who are now sheltering in overcrowded and unsanitary camps in Bangladesh," the group's medical director Sidney Wong said.
"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."
Rohingya refugees have told consistent stories of security forces and ethnic Rakhine Buddhist mobs driving them out of their homes with bullets, rape and arson that reduced hundreds of villages to ash.
Earlier this month the United Nations High Commissioner for Human Rights Zeid Ra'ad Al Hussein said the military-led crackdown appeared to include "elements of genocide."
Gunshot wounds were the cause of death in 69 percent of the cases, according to the survey. Another nine percent were reported burned alive inside houses, while five percent died from fatal beatings. For children under five, nearly 60 percent died after being shot, the survey found.
The estimate of the number of deaths announced by the group compares to Myanmar's government figure of 400 in September as a result of alleged attacks on police posts by Rohingyas.
Since Aug. 25, an estimated 613,000 Rohingya have crossed from Myanmar's western state of Rakhine into Bangladesh, according to the U.N.
The refugees are fleeing a military operation in which security forces and Buddhist mobs have killed men, women and children, looted homes and torched Rohingya villages. According to Bangladeshi Foreign Minister Abul Hasan Mahmood Ali, around 3,000 Rohingya have been killed in the crackdown.
Rohingya, described by the U.N. as the world's most persecuted people, have faced heightened fears of attack since dozens were killed in communal violence in 2012.
The U.N. documented mass gang rapes, killings — including of infants and young children — brutal beatings and disappearances committed by security personnel.
In a recent report, U.N. investigators said such violations may have constituted to crimes against humanity.