In some incidents it said women had been crucified and then had their throats slit.
The report quoted one female village chief, 51 year old Daw Way Way, who said taking on the role had been "similar to digging my own grave".
Like a third of the 95 women interviewed for the report, Daw Way Way said she was tortured by Myanmar government soldiers during her tenure.
According to the report the abuse often occurred as soldiers questioned villagers about their suspected ties to insurgents of the Karen National Union.
"Some of the villagers were arrested whilst working on their farms, they were tied up, crucified and finally had their throats cut," said Naw Pee Sit, another village chief who was beaten after being accused of such connections.
Although the UN and other organisations have documented similar atrocities against Myanmar's ethnic minorities, the country's military government has repeatedly denied allegations of abuses, saying its soldiers are only engaged in anti-terrorist operations.