Tanveer Hussain arrived in the small village of Saranac Lake in New York state for the World Snowshoe Championships.
Hussain was initially denied a visa, but managed to travel after campaigning by US activists and senators.
Police said he has been charged with first-degree sexual abuse, a felony, and endangering the welfare of a child, a misdemeanor.
Police arrested Hussain on Wednesday after the girl, who is under the age of 13, accused him of sexually abusing her, a report in the Adirondack Daily Entreprise said.
"He further was accused of touching her in an intimate area over her clothing," the statement said. "There was no accusation of force. The charges are a result of the age differences of the individuals. There were no other allegations made against Hussain," the statement said.
Police Sergeant Casey Reardon said the girl and her parents reported the abuse to police. It took place around Monday evening in the village. After the complaint, Reardon said police located Hussain who has been cooperating in the case, the report said.
Though India was not among the seven countries, the denial of visa was seen associated with the executive order.
Hussain was allowed a visa to enter the US for the competition following intense lobbying from local officials and residents in the Adirondacks, as well as by US Senators Kirsten Gillibrand and Charles Schumer.
Hussain was arraigned and his lawyer entered a not-guilty plea on Hussain's behalf.
"They are merely allegations alone. Not only is he innocent, he is presumed innocent by law. That is how he should be seen in the community and by anyone paying attention in this case," Barrett said.
Hussain and Khan had planned to return home this week. It said "a visibly upset Hussain", with hands shackled and still wearing a maroon World Snowshoe Championships hat, pleaded with the judge not to send him to jail, the report said.
"Sir, please. Help me," Hussain said.
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