The US-backed military campaign to retake Marawi claimed the lives of more than 1,100 people including around 900 militants, displaced 400,000 residents and reduced large parts of the city to rubble.
Amnesty called on Manila to investigate claims of "serious violations of international humanitarian law and other serious violations and abuses of human rights law" in a report on the violence, a month after President Rodrigo Duterte declared the city liberated from pro-IS gunmen.
"Philippine government forces violated the prohibition against torture and other ill-treatment of detainees, and allegedly committed the crime of pillage," the report said.
The rights group said it interviewed eight people, including seven Christian construction workers, who described how they were subjected to "sustained beatings and threats of execution" by Philippine marines.
Amnesty also said it spoke with several people who alleged that government forces looted civilian property of television sets, antiques, and computers while the militants stole weapons, jewellery and money from homes.
"Government forces may also have carried out disproportionate air and ground attacks," it said, adding that the civilian death toll from bombings and militant killings "is likely significantly higher than the official count".
Philippine military spokesmen in Manila and Marawi did not immediately respond to requests for comment by AFP.
Hundreds of local and foreign gunmen who had pledged allegiance to IS rampaged through Marawi, the principal Islamic city in the mainly Catholic Philippines, on May 23.
The rebellion was put down with the help of US and Australian surveillance planes and drones, with China and Russia also sending weapons to Filipino troops.
US Defence Secretary James Mattis last month praised the Philippine military for upholding human rights during the brutal urban battle.
But Amnesty said it had documented "a variety of serious violations of international humanitarian law by all parties" in the conflict.
Its report said witnesses described the militants killing at least 25 mostly Christian civilians, by shooting them or slitting their throats -- murders it described as war crimes.
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