In a new report, the watchdog revealed widespread discrimination by security forces, camp administrators and local authorities against women and children in eight camps for people displaced by violence.
"Iraqi women and children with perceived ties to Islamic State are being punished for crimes they did not commit," said Lynn Maalouf, Amnesty's Middle East research director.
Executions in Pakistan decline by 31pc in 2017: Amnesty International
"They are trapped in camps, ostracised and denied food, water and other essentials. This humiliating collective punishment risks laying the foundation for future violence."
The United Nations said in February that some 2.5 million people remained displaced after Iraqi forces backed by an international coalition waged a vast offensive to oust the extremist group from parts of northern Iraq it had seized in 2014. Many of those who fled Islamic State-held areas ended up in camps.
Amnesty said that in each of the eight camps it visited, women were being pressured into sexual relationships in exchange for money, aid and protection.
In its report, entitled "The Condemned: Women and Children Isolated, Trapped and Exploited in Iraq", the watchdog said women in the camps were also at risk of rape.
"The very people who are supposed to be protecting them are turning into predators," said Maalouf.
She called on the Iraqi government to show its commitment to protecting women by "holding all perpetrators to account and stopping all armed men from entering" the camps for the displaced.
Amnesty International decries 'intensifying' crackdown on freedom of expression in Pakistan
Amnesty also called on Iraqi authorities to "immediately end the systematic and widespread practise of forcibly disappearing men and boys with perceived ties to Islamic State that has left thousands of wives, mothers, daughters and sons in desperate situations".
In many cases, the men's only 'crimes' were escaping an IS stronghold, having similar names to terrorists on "wanted lists", or working in non-combat roles with the group, the watchdog said.
Iraq declared victory over Islamic State in December after pushing the militants out of their final holdouts along the border with Syria.
But the group retains the capacity to strike and still clings to pockets of desert in war-torn Syria.
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