Doctors Without Borders (Medecins Sans Frontieres or MSF) says its survey of refugee camps in Bangladesh put the death toll at around 9,000 between 25 August and 24 September.
It said 6,700 died as a result of the violence, adding that of those 730 were children under the age of five.
Myanmar's army has claimed 400 have died since the start of the crisis.
Myanmar's Information Ministry said the majority of fatalities were "extremist terrorists" who died during "clearance operations".
MSF medical director Sidney Wong said: "We met and spoke with survivors of violence in Myanmar, who are now sheltering in overcrowded and unsanitary camps in Bangladesh.
"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.
"The peak in deaths coincides with the launch of the latest 'clearance operations' by Myanmar security forces in the last week of August."
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He added that MSF's findings showed more than 59% of children below the age of five who were killed were reportedly shot, 15% burnt to death in their homes, 7% beaten to death and 2% killed in landmine blasts.
Around 630,000 Rohingya Muslims have fled Myanmar into Bangladesh to escape what the United Nations has called "ethnic cleansing".
They have been stripped of their citizenship, denied almost all rights, and labelled "stateless".
Romeo Dallaire, former commander of UN peacekeeping forces in Rwanda, told Sky News the crisis is "undoubtedly genocide".
He said: "It's as if they wrote the same book that the hardliners did in Rwanda and how the international community is reacting is following the same book, and this after the great pieces of work like Responsibility to Protect which we're all afraid to implement and operationalise."