The Guardian reported on Friday that senior figures associated with the Afghanistan women's team alleged that abuse took place inside the country, including at the federation's headquarters, and at a training camp in Jordan last February.
Interior Ministry spokesman Najib Danish said the government took the allegations very seriously and was examining the case.
"Based on a decision from the Attorney General's office, a team has been set up to investigate the case," he said.
The Afghan Football Federation rejected the allegation and warned that the report could lead to threats being made against members of the women's team. "Such allegations are baseless and we will have a thorough investigation," AFF Secretary General Sayed Aghazada told a news conference on Saturday.
Allegations of sexual contact outside marriage can have deadly consequences in Afghanistan. Victims of sexual harassment are often extremely reluctant to come forward for fear that they will be accused of adultery.
A spokesperson at FIFA, the world football federation, said it had a "zero tolerance" policy on abuse and was looking into the Afghan case but addressing the issue in a "do no harm way" towards the victims.
"As some aspects of these allegations involve sensitive topics linked to the protection of those involved, we have sought support from relevant parties who willingly offered their support to FIFA," the spokesperson said in an emailed statement.
"Once the facts are established whatever remedial measures needed will be taken."