The first comprehensive report on the "magnitude, frequency and brutality" of such violence in South Sudan's conflict zones was released by the International Rescue Committee and George Washington University's Global Women's Institute.
As the world's youngest nation approaches its fifth year of civil war, rape has often been used as a weapon by both government and opposition forces.
The civil war has killed more than 50,000 people, forced more than two million to flee abroad and plunged parts of the country into famine.
Up to 65 percent of women and girls interviewed for the new study said they had experienced sexual or physical violence, while over half of the women reported domestic abuse. In the capital, Juba, women and girls living in the United Nations-run civilian protection site were most vulnerable to sexual violence.
Chuol Madol said she was gang-raped by government soldiers in October when she left the camp in Juba to look for firewood.
"Women were crying but we were so deep in the bush that no one could help us," the 27-year-old told The Associated Press. "We're not fighting anyone. We're only here, trying to live."
The new report cites a "breakdown in the rule of law" in South Sudan, meaning perpetrators go unpunished.
"As we have seen in South Sudan time and again since this war started, armed forces on all sides engage in sexual violence with impunity. It is used both opportunistically and as a weapon of war to intimidate, punish and abuse civilians," said Jehanne Henry, senior Africa researcher for Human Rights Watch.
Civil society organisations are calling on South Sudan's government and UN agencies to create a "concrete strategy" for combatting the violence.
"Perpetrators of violence against women and girls in South Sudanese communities are multiplying regularly," said Edmund Yakani, executive director for the Community Empowerment for Progress Organization, a local advocacy group.
In light of the new UK-funded study, the British government has increased support aimed at helping 750,000 survivors in South Sudan and around the world to help "stop the cycles of violence."