Entitled ‘Left in the Dark,’ the report primarily focuses on air strikes and night raids carried out by US forces, including Special Operations Forces, and notes that apparent war crimes were not investigated and still remain unpunished.
Amnesty International Asia Pacific director Richard Bennett said: "Thousands of Afghans have been killed or injured by US forces since the invasion, but the victims and their families have a little chance of redress.
"The US military justice system almost always fails to hold its soldiers accountable for unlawful killings and other abuses.
"Evidence of possible war crimes and unlawful killings has seemingly been ignored."
The US military is accused of failing to criminally prosecute the soldiers involved in ten incidents that took place between 2009 and 2013, which claimed the lives of more than 140 civilians, including pregnant women and at least 50 children.
The report notes that war crimes were seemingly abundant in two of the case studies involving a Special Operations Forces raid on a house in Paktia province in 2010, and enforced disappearances, torture and killings in Nerkh and Maidan Shahr districts, from November 2012 to February 2013.
Since 2009, US military personnel have faced trials in six cases, despite unlawfully killing thousands of Afghan civilians, according to the organisation.
In the report, the US military or Nato were also found to be withholding further information about the progress of the investigation or its findings, after ensuring Afghan civilians that an investigation was being carried out.
Bennett said: "We urge the US military to immediately investigate all the cases documented in our report, and all other cases where civilians have been killed.
"There is an urgent need to reform the US military justice system. The US should learn from other countries, many of which have made huge strides in recent years in civilianising their military justice systems."
Amnesty also urged the Afghan Government to immediately establish its own mechanism to investigate abuses by Afghan soldiers and assume full combat responsibility by the end of the year.
Image: Amnesty’s report documents the failures of accountability for US military operations in Afghanistan. Photo: © Amnesty International.