In a report released amid continuing anger at the handling of sex cases in the wake of a deadly gang-rape in Delhi, the rights watchdog said the authorities had to become more sensitive towards victims.
"Children who bravely complain of sexual abuse are often dismissed or ignored by the police, medical staff and other authorities," said HRW's regional director Meenakashi Ganguly at the unveiling of the report.
"Instead, they subject the victim to mistreatment and humiliation."
The report details how children are sometimes forced to undergo a so-called 'finger test' to determine their sexual history, even though forensic experts say the examination has no scientific value.
It also quotes the mother of a three-year-old girl who was left in severe pain after being seen by doctors examining her alleged assault.
"For six to eight hours after the examination my daughter did not urinate because it was hurting her so much," the mother, who cannot be named, was quoted as saying in the report.
Ms Ganguly said it was this sort of "mistreatment" that needed to be addressed and called for an urgent overhaul of the criminal justice system.
Many of the criticisms contained in the report echo those voiced by protestors in the aftermath of the December 16 gang-rape that triggered demonstrations across the country and deep soul-searching about the handling of sex attacks.
The number of reports of sexual assault in India, whether attacks on children or adults, are believed to represent only a fraction of the overall number, with victims often too scared to file complaints.
"It is hard enough for a sexually abused child or their relatives to come forward and seek help, but instead of handling cases with sensitivity Indian authorities often demean and retraumatise them," Ms Ganguly told reporters.
"The failure to implement needed police reforms to be more sensitive and supportive to victims has made police stations places to be dreaded."
The 82-page report entitled "Breaking the Silence", contains more than 100 interviews on the experience of dealing with government institutions.
Child sexual abuse is common in homes, schools and residential care facilities across India and critics say the authorities have a poor record in bringing offenders to justice.
The most high-profile verdict saw two British men jailed for six years in 2011 for abusing several boys at a shelter they ran in Mumbai -- 10 years after charges were first filed.
Last year, the government enacted the Protection of Children from Sexual Offence Act which sets out punishments for all forms of sex abuse as well as guidelines for police and courts to deal with victims.
"It is a very good initiative from the government," Ms Ganguly said.
"But government efforts to tackle the problem will fail unless protection mechanisms are properly implemented and the justice system is reformed to ensure abuse is reported and fully prosecuted."