The 31-year-old man from Sri Lanka (identity withheld) was arrested over the weekend by police at the Regional processing centre at Lombrum.
The alleged incident took place on Jan 17 at the Harbour side Hotel between 8.30am and 4.30pm.
Manus acting provincial police commander, senior inspector David Yapu, said the victim is 19-years-old (identity withheld.)
It is alleged the defendant booked a room at the hotel where he sexually assaulted the victim.
PPC Yapu also said the victim managed to escape however, she fainted at the Lorengau river side on her way home.
She was later taken to the Lorengau General Hospital where she received treatment.