The 13-year-old girl, identified only as Angelica, was whisked by car from the airport to the Princess Anne Children’s Home, a government-run orphanage in the state capital Kota Kinabalu, the official said on condition of anonymity.
Angelica was wrongly deported to the Philippines in September along with thousands of Filipinos in a crackdown against illegal migrants in Sabah on Borneo island.
Initially thought to be a Filipino, the girl’s claim she had been raped at a detention center in Sabah provoked outrage in the Philippines.
Philippine President Gloria Arroyo shot a strongly-worded letter to Prime Minister Mahathir Mohamad asking him to immediately act on the complaint. A diplomatic protest was also lodged against Malaysia.
Investigations however revealed that the girl was a homeless Malaysian citizen living with illegal Filipino migrants in Sabah.
Malaysian Ambassador Taufik Mohamed Noor said Sunday the Angelica issue should be set aside as the neighbors continue to improve their bilateral relations.
Taufik offered assurances that Kuala Lumpur would take "all necessary steps for the probe in the rape case to proceed unhindered according to Malaysian laws and for justice to be rendered" to Angelica.