The two girls were found screaming and only partially clothed inside the Ship and Dock Inn motel room.
After being assessed by paramedics, the teenagers were found to have injuries consistent with sexual assault.
The girls were then transported to hospital for further treatment.
The man was arrested by the Sexual Assault Squad before being questioned and charged.
According to police, the two teenagers were abducted from the city on Sunday evening before being taken back to the room and attacked.
Police on Monday seized a lighter, head torch and note pad as evidence.
The 56-year-old man is set to face the Fremantle Magistrates Court on Tuesday on 10 separate offences including two counts of deprivation of liberty, five counts of sexual penetration without consent and two counts of unlawful and indecent assault.
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