According to the Women’s League of Burma, they have documented more than 100 cases, some involving children as young as eight.
Most r*pes were reportedly observed in areas where the army was still fighting armed ethnic groups.
However the government in Burma, also known as Myanmar, said using r*pe was not army policy and cases should be reported.
Most of the cases were linked to conflict in the border areas of Kachin and Northern Shan State.
The organisation provides that around 50% of cases were gang r*pes, and 28 women were killed or died of their injuries.
“Their widespread and systematic nature indicates a structural pattern: r*pe is still used as an instrument of war and oppression. s*xual violence is used as a tool by the Burmese military to demoralise and destroy ethnic communities,” the report reads.
Meanwhile presidential spokesman Ye Htut told Reuters news agency the military did not use r*pes as weapons and were trying to take effective measures against the offenders.
President Thein Sein has introduced major reforms since the elections of November 2010, which saw military rule replaced by a military-backed civilian government.
The last three years have seen far-reaching political change in Burma, but the army has so far shown little appetite for change, or altering the way it operates, says the BBC’s Jonah Fisher in Rangoon.
A new round of talks is due to start later this month aimed at achieving a cease-fire in all of Burma’s ethnic conflicts, our correspondent adds.