The abuses are encouraged by a weak judicial system and the failure of all levels of government in Africa's most populous country to tackle the abuses, the group said in a report titled ''Nigeria: Rape - the silent weapon.''
Soldiers in Nigeria still enjoy a large measure of impunity seven years after the election of President Olusegun Obasanjo ended 30 years of almost continuous army dictatorship.
``The harsh reality is that if you ... suffered the terrible experience of being raped, your suffering is likely to be met with intimidation by the police, indifference from the state and the knowledge that the perpetrator is unlikely to ever face justice,'' said Amnesty's Africa Director Kolawole Olaniyan.
Drawing on the testimony of survivors, the report identifies disturbing trends of rape and sexual violence against women and says impediments to the reporting and prosecuting of rape cases in Nigeria include inadequate training of police.
This results in the humiliation and intimidation of victims and investigations hampered by corruption and incompetence, the report said. Only about 10 percent of cases are successfully prosecuted, it added.
RAPISTS DON'T HIDE
One woman who was not named in the report told Amnesty how she, her 12-year old daughter and sister were all raped by military men.
``Everyone in the village saw them, they didn't hide, they didn't care. I didn't tell the police because I fear them,'' the report quoted the victim as saying.
Differences between federal and state law, and between Islamic Sharia law in the north and tribal law in the south, have led to uneven standards of justice and arbitrary decisions, the report said.
``The Nigerian government has taken no meaningful action to translate its international legal obligations toward women and girls into national law, policy and practice,'' Olaniyan said.
``It is now time that the state and federal authorities meet those obligations and offer real security and justice to women and girls in Nigeria,'' Olaniyan added.
Nigerian security forces and police continue to face heavy criticism despite the end of military dictatorship in the world's eighth largest oil exporter.
In March, a U.S. Department of State report accused the security forces of carrying out political murders and other extra-judicial killings in 2005, and using excessive force in their actions against criminal suspects or protesters.
The report said troops and police committed other serious human rights abuses including extortion, torture and unlawful detention of criminal suspects.
In 2005, Human Rights Watch called on Western donors funding police reform in Africa's top oil producer to link continued aid to measurable steps to curb the torture and killing of suspects.