Several prisoners, mostly civilians accused of links to opposition or rebel groups but who have not been charged, have died from the punishment, the rights group said. Soldiers have also beaten the prisoners, Amnesty added.
“Detainees are suffering in appalling conditions and their overall treatment is nothing short of torture,” said Muthoni Wanyeki, Amnesty International’s chief in East Africa, adding that prisoners are “fed only once or twice a week and given insufficient drinking water.”
There was no immediate response from South Sudan’s army, who denied previous reports they suffocated prisoners in similar shipping containers last year.
In South Sudan, metal containers are often used as makeshift prison cells. Temperatures in can easily top 40 degrees Celsius (104 degrees Fahrenheit).
Amnesty said the prisoners were held in a basic prison site called Gorem, some 20 kilometres (12 miles) south of the capital Juba.
Satellite images released of what they believe is the prison site show four metal shipping containers arranged in an L-shape inside a double perimeter fence.
“All detainees should be released or charged and brought before independent courts,” Ms Wanyeki said, adding that most are civilians who “have not been charged with any offence.”
In October 2015, government troops killed at least 50 people in the town of Leer by stuffing them into a shipping container in baking heat, according to ceasefire monitors from the internationally-backed Joint Monitoring and Evaluation Commission (JMEC).
The government denied those killings, but Amnesty investigators later spoke to 23 eyewitnesses who saw the men and boys forced into the container with their hands tied or saw the bodies later dragged away and dumped.
READ: South Sudan troops accused of suffocating 50 people in container
Civil war erupted in South Sudan in December 2013 but rebel chief Riek Machar returned to the capital last month as part of a peace deal which saw him become vice-president, forging a unity government with President Salva Kiir.
However, fighting continues among multiple militia forces who now pay no heed to either Kiir or Machar.
All sides have been accused of perpetrating ethnic massacres, recruiting and killing children and carrying out widespread rape, torture and forced displacement of populations to “cleanse” areas of their opponents.