The human rights group said it has “credible evidence” that around 10,000 Turkish soldiers face the severe punishments for their part of the failed military coup against president Erdogan.
Victims are being held in makeshift cells, such as stables and sports halls, and are being tortured and held in stress positions for 48 hours, the group said.
Shocking pictures have emerged on social media appearing to show detained soldiers in cramped, inhumane conditions.
Amnesty’s European director John Dalhuisen said: “Reports of abuse including beatings and rape in detention are extremely alarming, especially given the scale of detentions that we have seen in the past week.
“The grim details that we have documented are just a snapshot of the abuses that might be happening in places of detention.”
A lawyer working at the Caglayan Courthouse in Istanbul said she saw a detainee attempting to jump out of a sixth floor window and another banging his head against a wall.
The non-profit organisation has asked for access to prisoners who have been rounded up and arrested in the wake of the failed coup.
Dalhuisen said: “It is absolutely imperative that the Turkish authorities halt these abhorrent practices and allow international monitors to visit all these detainees in the places they are being held.”
“Reports of abuse including beatings and rape in detention are extremely alarming, especially given the scale of detentions that we have seen in the past week.”
More than 290 people died on the night of the bloody coup with Erdogan calling a three month state of emergency.
The democratically elected leader muted at the possibility of reinstating the death penalty, something which has been condemned by the international community and would all but end Turkey’s chances of EU membership.