The New York-based rights group said in a report on Thursday that National Intelligence and Security Service (NISS) regularly arrests opposition politicians and rights workers across Sudan.
However, female rights women involved in protests and rights campaigns, including students, teachers, lawyers and journalists faced additional dangers from the security services, it noted.
"Women engaged in these efforts are targeted with a range of abuses, from rape and rape threats, to deliberate efforts to tar their reputations. Their male counterparts may be less likely to experience some of these abuses," HRW said in the report, adding, "Many women said they felt that they had no choice but to abandon their work or flee the country, leaving careers and family behind."
The international rights group says it had documented numerous instances of security officers raping or threatening sexual violence against women campaigners.
Meanwhile, HRW Africa director Daniel Bekele has said that NISS officers were able to take advantage of social conventions and "discriminatory laws to silence" women activists.
"Sudanese women who defend human rights experience political repression like their male colleagues but are also vulnerable to sexual assault and intimidation because they are women," said Bekele, adding, "Sudanese security officials often take advantage of discriminatory laws and social conventions to silence them."
The HRW official went onto say that no security officer has been prosecuted for rape, sexual assault, or harassment of activists.
According to HRW, abuse of women has increased in recent years along with the rise of protests following the Arab Spring, South Sudan's secession from Sudan in 2011 and Sudan's economic downturn.
Sudan's security forces have wide-ranging powers and are immune from prosecution.