The comments by Alice Wells, US assistant secretary of state for South and Central Asia, come after British newspaper The Guardian last month detailed accounts of the abuse, which allegedly affected more than 500 victims in Logar province south of Kabul.
"We call on Afghan authorities, including the Attorney General's Office, to take decisive action on deeply troubling reports of sexual abuse in Logar schools," Wells wrote on Twitter.
The alleged abuse comes amid an ongoing tolerance of paedophilia and pederasty in some parts of Afghanistan, including the practice of bacha bazi, or "boy play", where older men make boys dress up as women and then rape them.
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"Sexual violence and practices like bacha bazi have no place in any society," Wells said.
President Ashraf Ghani's spokesperson Sediq Sediqqi said the Afghan government is "strongly committed to taking decisive actions" in the case, following a full probe.
"Law enforcement entities will hold the perpetrators accountable," Sediqqi said on Twitter.
The scandal has generated international outrage that was only fuelled by the authorities' initial reaction.
The National Directorate of Security (NDS) arrested two whistleblowers in the case and said their "baseless" claims were part of a scheme aimed at securing asylum in a foreign country.
It was only after Ghani intervened that the NDS released the two men.
In 2017, Afghanistan introduced measures that criminalised the sexual abuse of minors, following reporting on bacha bazi by several media outlets including AFP.
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However, children are often reluctant to come forward in a culture that still shames victims rather than going after perpetrators.
The US has previously come under criticism for treading softly around the issue of Afghan child abuse.
According to a watchdog report in January 2018, the US military funded Afghan police and security units even though American officials knew members were implicated in gross human rights violations, including child sexual assault.
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