In a 48-page report, the US-based rights organization cast doubt over Khartoum's repeated denials that a mass rape took place in October in the town of Tabit.
At least 221 women and girls were raped when the Sudanese army launched three waves of attacks over 36 hours, beginning on October 30, according to the report, based on accounts from dozens of Tabit residents.
Soldiers went from house to house, looting property, beating residents and arresting men who were taken to the outskirts of the town while women and girls were raped inside their homes, HRW said.
The army rampage on Tabit may have been in retaliation for the abduction of a soldier or to punish residents for their support of rebel armed groups in recent years, the report said.
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Two army defectors told HRW that they had been ordered by their superior officers to rape women because they were rebel supporters even though there were no fighters near Tabit at the time of the attacks.
Khartoum has repeatedly denied the rape allegations but has refused to allow the United Nations-African Union force in Darfur, UNAMID, to carry out a full investigation.
But an internal report from the mission obtained by AFP in November said the Sudanese military had tried to intimidate villagers to suppress the allegations.
HRW urged the International Criminal Court (ICC) to open an investigation of the mass rape, which it said would amount to crimes against humanity if found to be part of a widespread or systematic attack on the civilian population.
The report quoted a woman in her 40s whose three daughters were raped in their house, two of whom were under the age of 11.