The report in the British newspaper on Friday cited senior figures associated with the team as saying the abuse took place at the federation's headquarters in Kabul and at a training camp in Jordan last February.
The Guardian also cited Khalida Popal, a former head of women's soccer in the Afghanistan Football Federation who was forced to flee the country in 2016 and seek asylum in Denmark, as saying that her own investigation uncovered physical and sexual abuse, death threats and rape.
Ghani described the report as "shocking to all Afghans," the presidential palace said. On Monday night, he met with officials from the Afghan National Olympic Committee, sportsmen and sportswomen, and pledged authorities would "conduct a thorough investigation into this."
Attorney General Farid Hamedi promised a transparent probe.
"I would like to assert in front of our athletes, the president and people of Afghanistan that we will proceed with this investigation transparently, justly and comprehensively," said Hamedi.
Sayed Alireza Aqazada, AFF's secretary-general, denied the allegations in the Guardian report, saying they were "all baseless and untrue." Hafizullah Wali Rahimi, president of Afghanistan's Olympic Committee, told local media that such allegations were not new and that there had been similar complaints in the past.
"Even if mere allegations (of abuse) cause our people to stop sending their sons and daughters to sports, we need to act immediately," said Ghani. "We have to have a framework in place to mitigate such incidents in our sports."
Danish sportswear brand Hummel cancelled its sponsorship of the Afghan team last month, calling for new leadership of the soccer federation. It said the decision was made after "allegations of severe mental, physical and sexual abuse as well as documentation of new contracts stripping female players of basic human rights was presented to the company."
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