The girl was sent to the shelter house in June when her mother was detained on a drug charge.
The mother was released from prison last week and contacted the shelter house to get her daughter back. They were reunited on Thursday afternoon.
The mother told police that later that night the girl became sick, so she took her to Banglamung Hospital early Friday morning.
Doctors who examined the girl found that she had a fever and had been assaulted, with bruises on her body and bleeding from her vagina and anus.
The girl told her mother that she has been raped by several senior boys almost every day when she was at the shelter house. Even on her last day there she was raped in the morning, the mother alleged.
Pol Col Supachai Phuikaewkam, superintendent of Banglamung Police Station, said the mother, 42, was distraught when police met her at the hospital and extremely upset about the cruelty inflicted on her young daughter.
She told police that she had been working at a bar in Pattaya when she was detained by police on a drug charge two months ago. She asked her cousin to take the child to stay at a shelter house in tambon Rongpo of Banglamung district.
Pol Col Supachai said police and social workers will investigate the case and find the alleged rapists. He added that the shelter should be a safe place for children and that the abuse of the young girl was a direct contradiction of the purpose of the establishment.