A study by Human Rights Watch (HRW) found the banned "two-finger test" - which involves a doctor inserting fingers into a rape victim's vagina to determine if she is sexually active - being carried out at a hospital in Rajasthan.
"In some states, both the police and the medical system have not adopted the measures the government set out," Meenakshi Ganguly, South Asia director at the US-based advocacy group told the Thomson Reuters Foundation.
"While the intention is there (to help rape survivors), it does not percolate down the system."
Home ministry officials said they could only comment once they had seen the report.
India has some of the highest number of rapes in the world but many sex crimes are not reported, offenders often go unpunished and the wheels of justice turn slowly, activists say.
The HRW analysed the impact of reforms introduced following the gang-rape of a student in a Delhi bus in 2012 that led to national outrage and put a global spotlight on rape in India.
Nearly 35,000 rape cases were reported to the police and 7,000 convictions made in 2015, both increasing by about 40 percent in three years, according to government data.
But access to support services, ranging from legal aid to healthcare, is poor and gender-friendly government guidelines are often flouted, HRW said.
India's top court said in 2013 that the two-finger test violated a woman's right to privacy.
It was banned and the Indian Council of Medical Research issued new guidelines in 2014.
But the HRW found the test mentioned in a form that doctors fill in when they examine rape survivors at a Rajasthan hospital.
Sexual violence remains a taboo in the world's largest democracy, and women fear stigma or retribution if they report attacks.
The HRW called for India to introduce a victim and witness protection system to encourage people to come forward.
It interviewed more than 20 rape survivors, as well as lawyers, doctors and police officials in four states with a high prevalence of rape, as well as New Delhi and Mumbai.
Reporting by Roli Srivastava @Rolionaroll; Editing by Katy Migiro.