The London-based organisation, which released a report on the issue, also said that the Pakistani government should reinstate judges deposed by President Pervez Musharraf.
"Prime Minister Yousuf Raza Gilani has emphasised the coalition government's commitment to upholding human rights," said Sam Zarifi, Amnesty's Asia-Pacific director.
"We urge him to act immediately to resolve all cases of enforced disappearance."
Amnesty cited local Pakistani organisations saying there were at least 563 cases of enforced disappearance.
Using court records, affidavits of victims and witness testimony, Amnesty claimed government forces would detain individuals, including one nine-year-old boy who was held to make his wanted brother turn himself in, and move them between detention centres to make it harder for their whereabouts to be traced.
It also said government officials obstructed attempts to find out where those who had disappeared had gone. The human rights group also called on foreign governments to ensure they were not complicit in the practice.
"We don't know if those subjected to enforced disappearances are guilty or innocent, but it is their fundamental right to be charged and tried properly in a court of law," Zarifi said.
"By holding people in secret detention the government of Pakistan has not only violated their rights, but also failed in its duty to charge and try those suspected of involvement in attacks on civilians."
