In a report, it said that women were punished for fleeing domestic abuse and violence while some rape victims were also imprisoned.
Sex outside marriage – even when the woman is forced – is considered adultery, another “moral crime”.
The I Had to Run Away report was released in Kabul on Wednesday.
The report said that the government of President Hamid Karzai had failed to fulfil its obligations under international human rights laws.
“It is shocking that 10 years after the overthrow of the Taliban, women and girls are still imprisoned for running away from domestic violence or forced marriage,” HRW Executive Director Kenneth Roth said.
The report called on the government to release about 400 women and girls held in jails or juvenile detention centres.
Earlier this month the president endorsed a “code of conduct” issued by an influential council of clerics which allows husbands to beat wives under certain circumstances.