The previously secret report, first provided to Congress in June but now declassified, lays bare the cultural rifts that can exist when America works with local partners.
US lays out 'concrete' steps for Pakistan: Pentagon
According to the report by the office of the Special Inspector General for Afghanistan Reconstruction (SIGAR), the Pentagon repeatedly granted exemptions from US rules that bar assistance to a foreign nation's security forces if credible information exists of rights violations.
For instance, the Pentagon approved waivers to these so-called Leahy Laws to continue funding for 12 Afghan security force units implicated in 14 gross human rights violations in 2013.
The same workaround, known as the "notwithstanding clause," was used for eight of nine additional units implicated in 2014.
Although the Defense Department and State Department have "confirmed that some units of the Afghan security forces have committed gross violations of human rights, the secretary of defense has used the notwithstanding clause" to some implicated units, the report states.
The exemptions were made under then-secretaries Chuck Hagel and Ash Carter.
In a response to the report, the Pentagon said the document "does not reflect an understanding of the challenges faced by US forces in Afghanistan in developing and sustaining the Afghan National Defense and Security Forces".
Jedidiah Royal, a Pentagon official, wrote that removing the "notwithstanding clause" would remove the defense secretary's ability to balance the Leahy Laws with "national security objectives and the protection of US forces".
The report states that as of June 12, 2016 officials were tracking 75 reported gross violation of human rights incidents, including seven involving child sexual assault.
Afghanistan has an entrenched custom of what is known as "bacha bazi" - or the sexual abuse of boys - and critics have long accused the United States of not doing enough to counter it.
In one instance outlined in the report, a US soldier heard Afghan men screaming "in what sounded like sex" but did not take action to report it, SIGAR states.
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"The full extent of child sexual assault committed by Afghan security forces may never be known," the report says.
In addition to the child sex assault incidents, officials were also tracking extrajudicial killings and the torture of detainees.
Members of Congress requested the review in 2015 after The New York Times reported on 'rampant' child sex abuse in the Afghan security services and said that US personnel had been told not to intervene.
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