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The aid group interviewed several thousand Rohingya refugees in four camps in Bangladesh in late October and early November, asking how many members of their families had died and how, both before and after the violence began.
The survey showed that a minimum of 6,700 Rohingya -- including 730 children -- were killed by shooting and other violence between August 25 and September 24, and that at least 2,700 others died from disease and malnutrition, according to MSF.
The aid agency's death toll far surpasses estimates from Myanmar's government, which has put the figure in the hundreds.
More than half a million Rohingya have fled northwestern Myanmar into Bangladesh since a concerted military crackdown began in late August, following militant attacks on a border post. Both the UN and the US have described the campaign as ethnic cleansing.
"We met and spoke with survivors of violence in Myanmar, who are now sheltering in overcrowded and unsanitary camps in Bangladesh," Sidney Wong, MSF's medical director, said in a statement. MSF also is known as Doctors Without Borders.
"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."
He said that the "peak in deaths coincides with the launch of the latest 'clearance operations' by Myanmar security forces in the last week of August."
Zaw Htay, a Myanmar government spokesman, did not respond to a request for comment on the MSF report.
The Rohingya are a stateless Muslim minority in Myanmar's Rakhine state thought to number about 1 million people. Myanmar does not recognize them as citizens or as one of the 135 recognized ethnic groups living in the country.
Stories of horror
"They killed and killed and piled the bodies up high. It was like cut bamboo," said Mumtaz, a Rohingya woman from the village of Tula Toli in western Myanmar, who woke up to find herself on a mound of charred bodies.
"In the pile there was someone's neck, someone's head, someone's leg. I was able to come out, I don't know how."
A report commissioned by Myanmar's military into the crisis cleared the army of wrongdoing, denying widespread reports of murder, rape and destruction in Rakhine state.
"There is overwhelming evidence that the military has murdered and raped Rohingya and burned their villages to the ground," Amnesty said.
The Myanmar military report attributed the mass exodus of refugees and the repeated reports of military violence to a campaign of misinformation perpetrated by the Rohingya militant group Arakan Rohingya Salvation Army (ASRA).
'Likely an underestimation'
According to the MSF news release, the overall Rohingya death toll during the 31 days following the start of violence could be as high as 13,759, including at least 1,000 children under the age of 5.
Gunshots were the cause of death in 69% of the violence-related killings, followed by being burned to death in their houses (9%) and beaten to death (5%). Of the children under 5 who died during that period, 2% were killed by landmines.
"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," Wong said.
"We heard reports of entire families who perished after they were locked inside their homes, while they were set alight."