Some have been forced to give birth at Israeli checkpoints because they are not allowed through to hospitals, while others are subject to "honour killings" by relatives.
The human rights group said women in the occupied West Bank and Gaza Strip were increasingly the victims of both sides in the Israeli-Palestinian conflict.
"Palestinian women have borne the brunt of the escalation of the conflict and decades of Israeli occupation, while in Palestinian society they are subjected to a system of laws and norms that treats them as unequal members of society," it said.
Occupation and patriarchy
The report, which was issued on Thursday, entitled "Conflict, Occupation and Patriarchy: Women Carry the Burden", is part of Amnesty's campaign to end violence against women.
It paints a stark picture.
Border restrictions coupled with the resurgence of traditional tribal rules have made it difficult if not impossible for women and girls at risk to escape honour killings for having sullied the family name, Amnesty said.
The disintegrating rule of law within areas governed by the Palestinian Authority means the perpetrators of such crimes go largely unpunished, it added.
Women have been forced to give
birth at Israeli checkpoints
"Although there are no reliable statistics, violence against women in the family, including sexual abuse, rape and so-called honour killings ... have reportedly increased in the past four and a half years," the report said.
"But often those responsible for such killings have not been brought to justice."
Amnesty said more than 3200 Palestinians including 600 children and 150 women had been killed by the Israeli army in the uprising, while more than 1000 Israelis including 100 children and 200 women had been killed by armed Palestinian groups.
The Israeli security clampdown had produced unprecedented levels of poverty, unemployment and rising health problems among Palestinians - particularly women, Amnesty said.
"Scores of women have been forced to give birth at checkpoints by the roadside and several have lost their babies because Israeli soldiers denied them passage," it said.
"I crawled behind a concrete block by the checkpoint to have some privacy and gave birth there, in the dust, like an animal"
It cited the case of Rula Ashtiya who was refused passage on 26 August 2003, by Israeli soldiers at the Bait Furik checkpoint on the way to hospital in Nablus to give birth.
"I was lying on the ground in the dust and I crawled behind a concrete block by the checkpoint to have some privacy and gave birth there, in the dust, like an animal," she said.
"I held the baby in my arms and she moved a little but after a few minutes she died in my arms."
Amnesty said the soldiers' refusal to let her pass contravened the Geneva Conventions, which applied to Israel as the occupying power, and urged the Israeli authorities to lift the blockades and movement restrictions on Palestinians.
At the same time, the Palestinian Authority's own security apparatus had to not ensure only that women were not subject to victimisation, violence and honour killings but that perpetrators were brought to justice, the group said.