The abuse includes young girls being forced into marriages or bartered to settle debts, the UN said.
UN women's rights monitor Yakin Erturk on Monday urged the government to do more to protect women and said ignoring the issue because of fears it could cause political instability "not only falls short of the United Nations' founding principles, but is also politically shortsighted".
"Stability in Afghanistan can only be secured if the social fabric is rewoven from the grass roots," she said.
"This in turn requires an end to the state of violence and impunity, of which the pervasive, intense violence experienced by Afghan women at all levels is a central but neglected element."
Speaking at a news conference in the capital, Kabul, after a 10-day visit, Erturk said poverty, lack of education and decades of conflict had worsened the plight of women.
"For the great majority of girls and women there is no alternative to enduring the violence they encounter," she said.
"Giving little girls away for bride money and exchanging daughters to settle disputes are just some practices condemning girls to a life of despair."