The UN earlier announced it was sending a team to Iraq to investigate “acts of inhumanity on an unimaginable scale”.
IS and allied Sunni rebels have seized large swathes of Iraq and Syria.
Thousands of people have been killed, the majority of them civilians, and more than a million have been forced to flee their homes in recent months.
An Amnesty report released on Tuesday said it had gathered proof that several mass killings took place in the northern region of Sinjar in August.
Two of the deadliest took place when IS fighters raided villages and killed hundreds of people on 3 August and 15 August.
“Groups of men and boys including children as young as 12 from both villages were seized by IS militants, taken away and shot,” the UK-based group said.
“IS is carrying out despicable crimes and has transformed rural areas of Sinjar into blood-soaked killing fields in its brutal campaign to obliterate all trace of non-Arabs and non-Sunni Muslims.”
Analysis: Jim Muir, BBC News, Irbil
Unlike almost any armed faction in history, Islamic State (IS) militants go out of their way to advertise and publicise their most atrocious deeds on the internet.
They include the mass murder of hundreds of Shia soldiers or militia captured in Tikrit, the similar fate dealt to scores of Syrian troops taken prisoner after the fall of Tabqa airbase last month, several filmed decapitations – including US journalist James Foley – and many other blood-curdling incidents.
The goal is clearly to strike fear into their opponents, a tactic that, combined with lightning strikes out of the blue, has certainly triggered panic and flight in some places.
But some of their opponents have dismissed all this as psychological warfare. Syrian Kurdish fighters have been clashing with IS for over a year without help, often defeating them. Iraqi Kurdish, Shia and government forces are also starting to push back, with a little help from outside friends.
On Monday, the United Nations Human Rights Council agreed to deploy an emergency mission to investigate crimes allegedly carried out by IS.
Deputy Human Rights Commissioner Flavia Pansieri warned that IS (formerly known as Isis) was targeting Christian, Yazidi, Turkmen, Shabak, Kaka’i, Sabean and Shia communities “through particularly brutal persecution”.
Meanwhile, Iraqi Shia militias and Kurdish forces have continued their advance against IS, seizing the militant stronghold of Suleiman Beg on Monday.
Earlier, the joint forces had broken a two-month siege by IS fighters in the northern town of Amerli.
The militias said Iran had played a role in the recent operations, supplying weapons and helping with military planning.
Thousands of minority Shia Turkmen had been holding out in Amerli, and the UN had expressed fears there could be a massacre if IS captured it.
The BBC’s Gabriel Gatehouse, who entered the town on Monday, found residents happy to be reunited with their families.
They told him there was a huge amount of work to do to get back to normal.
Our correspondent says there are still pockets of IS resistance in the area, meaning that travel to the town remains problematic.
Outgoing Prime Minister Nouri Maliki visited Amerli on Monday, saying: “Our enemy is retreating and our security forces backed by volunteers are advancing to purge further towns.”
Correspondents say the recent advances are the biggest success by Iraqi and Kurdish forces against IS in recent months.
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