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The victim told investigators that she woke up to find her pants and shirt unbuttoned and the mans hand inside her pants.
The victim went to the back of the plane to report the incident to a flight attendant, the criminal complaint was quoted as saying by the report.
Ramamoorthy was arrested after the plane landed, according to court documents.
He said in a written statement that he had taken a pill and fallen into a deep sleep, and that he hadn't done anything.
Magistrate Judge R Steven Whalen, who said it was a "very unusual case", ordered Ramamoorthy to be held pending trial after the Federal prosecutor successfully argued that he was a flight risk and a potential danger to others around him.
"It seems that shes either colluding with the defendant to cover up his actions or shes completely oblivious to what he did," the prosecutor argued.