The batsman was arrested in November last year just hours after his country lost to England in their final Twenty20 World Cup match in Australia.
He was accused of four counts of sexual intercourse without consent after arranging to meet a woman at a bar near the Sydney Opera House through a dating app.
"The complainant was fearing for her life and could not get away from the accused," police alleged in a facts sheet cited by local media, having gone back to her home.
Three of the charges, relating to non-consensual oral and digital penetration, have now been withdrawn, media cited prosecutors as saying.
Gunathilaka, who is on bail, is set to reappear in court to make a plea on July 13th.
He made his international debut in 2015 and has played eight Tests, 47 ODIs and 46 T20s. Sri Lanka Cricket suspended him after he was charged.
