The figure is the highest estimated death toll yet of violence that erupted on August 25 and triggered a massive refugee crisis, with more than 620,000 Rohingya fleeing Myanmar for Bangladesh in three months.
The UN and US have described the military operation as ethnic cleansing of the Muslim minority, but have not released specific estimations of a death toll.
"At least 6,700 Rohingya, in the most conservative estimations, are estimated to have been killed, including at least 730 children below the age of five," MSF said Thursday.
The group's findings come from six surveys of more than 2,434 households in Rohingya refugee camps and cover a period of one month.
"We met and spoke with survivors of violence in Myanmar, who are now sheltering in overcrowded and unsanitary camps in Bangladesh," said the group's medical director Sidney Wong.
"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."
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.
Myanmar's army has denied any abuses and says only 400 people -- including 376 Rohingya "terrorists" -- died in the first few weeks of the crackdown.
But MSF said the peak in deaths coincided with the launch of "clearance operations" by the army and local militias in late August, and were evidence "that Rohingya have been targeted".
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