Around 400 people join makeshift shelters around the country every day, Amnesty said in a report entitled "Fleeing war, finding misery", based on three years of research.
The Afghan government estimates that more than 40 people froze to death this winter, the harshest in 15 years, with at least 28 children dying in camps around Kabul.
The government is "not only looking the other way but even preventing help from reaching them" in an attempt to avoid making the settlements permanent, Amnesty researcher Horia Mosadiq said.
"Local officials restrict aid efforts because they want to pretend that these people are going to go away. This is a largely hidden but horrific humanitarian and human rights crisis," she said.
The report calls on the government to remove conditions placed on humanitarian assistance and on international donors to "ensure that their humanitarian assistance addresses the needs of internally displaced people".
Kabul alone houses up to 35,000 displaced persons in 30 slum areas around the city, according to the report.
Most slum residents told Amnesty that they had fled their homes to escape the escalating war which has seen the number of civilian deaths rise steadily to a record of more than 3,000 in 2011, according to UN figures.
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