The African nation has suffered five years of brutal civil war and, despite a fragile peace accord signed two months ago by the government and rebel groups, remains split with ethnic grievances and awash with weapons.
Civilians from rival groups often bear the brunt of the violence and cycle of revenge.
As well as rape, survivors of the violence in the the Northern Liech State's town of Bentiu, also reported being whipped, beaten and clubbed with sticks and rifle butts, MSF said in a statement.
It added that they were also robbed of money, clothes, shoes and food ration cards.
“Some [of those raped] are girls under 10 years old and others are women older than 65. Even pregnant women have not been spared from these brutal attacks,” said MSF midwife Ruth Okello.
However, the Northern Liech State's minister for information disputed the veracity of the reports.
“A rape of such a magnitude is not true,” Lam Tungwar said. “We are a state [that] respects human rights and women’s rights top our list.”
Mr Tungwar said local courts would tackle the cases of violence in Bentiu and other counties, but added: “I don’t concur with the current report because it doesn’t portray us and the community in Northern Liech state.”
South Sudan’s president, Salva Kiir, signed a peace agreement with rebel factions in September to end the country’s civil war, which erupted in 2013 and has killed around 400,000 people and forced a third of the population from their homes.
Previous peace deals have quickly fallen apart.
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