The report published by the Euro-Mediterranean Human Rights Network (EMHRN) documents what it describes as "arbitrary" detentions and contains testimony from dozens of former prisoners.
"Women have been increasingly weaponised in Syria's ongoing bloody war, with dire repercussions for the country's social fabric and the prospect of ending the conflict," the report wrote.
EMHRN released the report on the eve of a meeting in Geneva on Tuesday of the UN Rights Council which is expected to address the rights situation in Syria.
The 42-page report, entitled "Detention of Women in Syria: A Weapon of War and Torture", documents the cases of pregnant women held in jail and of mothers imprisoned with children under the age of 18.
The report details "horrendous violations perpetrated against women by the Syrian government... in a widespread and systematic manner, as well as the use of women as bargaining chips in hostage exchanges with anti-governmental armed groups".
Women held in Syrian government prisons are subjected to "various forms of deprivation, threats, solitary confinement, as well as different forms of torture, including rape and sexual harassment", it said.
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Their ordeal continues long after they are freed, it said, citing people sacked from their jobs, others who were rejected by their families or forced to divorce their husbands.
Laila, a 38-year-old activist and mother of two jailed in 2013, recalled her interrogation "in a cold room full of rats" saying she was made to stand naked and was menstruating at the time.
Another prisoner, Sawsan, said she was raped by 10 members of the security forces -- the first time in front of her 16-year-old son.
Other women said they were forced to make false confessions and to say they had practised "jihad sex" with rebels fighting the regime.
EMHRN president Michel Tubiana urged the international community to exert "intense efforts" to help such women.
"Intense efforts need to be made at international level in order to provide women who have been exposed to grave violations with adequate rehabilitation and protection mechanisms," he said.
The Britain-based Syrian Observatory for Human Rights estimates that more than 200,000 people, including thousands of women, are held in Syrian regime detention centres.