Running away from home, usually from abuse and forced marriage, and alleged adultery, which often involves rape, have landed most of the 600 women in prison. That figure is an increase of 50 percent over the last 18 months.
"That increase reflects a shameful lack and failure of political will by both the government of Afghanistan and its foreign donors and allies," Phelim Kine, HRW's deputy director of Asia, told reporters.
Women have won back rights of education and work since the Taliban were toppled by U.S.-backed Afghan forces in late 2001, but there are fears these freedoms could be curtailed after most NATO-led forces leave by the end of next year.
Rights workers and some Afghan female lawmakers accuse President Hamid Karzai's government of doing too little to protect women - allegations his administration denies.
The New York-based rights group said the statistics on girls and women in prison came from the Interior Ministry.
The findings come days after parliament failed to ratify an Elimination of Violence Against Women law, which would have strengthened a 2009 presidential decree banning forced and underage marriage, beatings and rape.
Conservative religious lawmakers blocked the decree's ratification, arguing some articles were un-Islamic, such as keeping the legal age for women to marry at 16 and maintaining the existence of shelters for domestic abuse victims.
Barr said if the abuse of girls and women continued, countries that help Afghanistan might not be willing to.
"International donors will not support a country where girls who are 9 or 10 years old can be married," she said.
While HRW said it was difficult to pinpoint the reason for the increase in the imprisonment of women for "moral crimes", Barr said incarceration of both men and women had risen across the country in recent years.
The pending withdrawal of foreign troops and dwindling global interest in Afghanistan may also play a role.
"As everyone anticipates the departure of foreigners, there is a feeling that, in a sense, things can go back to normal," she said.
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