The new policy, decided at a two-day conference in Bangkok that ended yesterday, will remove boys aged 12 and older from the shelters, Phuketwan has learned.
The policy is likely to further splinter Rohingya families where men are already held in police cells and Immigration detention centres and their wives and children in family refuges.
Girls and boys are also likely to be separated within family shelters. Men seem certain to be barred from entry, while officials are looking at appointing female security guards, Phuketwan has been told.
The rape that has the Ministry of Social Development and Human Security radically altering its rules took place at a shelter house in Chonburi's Banglamung district, according to a report in the Bangkok Post.
The four-year-old girl told her mother that she has been raped by several senior boys from June on, when her mother was detained on a drug charge.
When the mother was released from prison in late August and contacted the shelter to get her daughter back, the girl told her mother that she has been raped by several senior boys almost every day.
It is believed the boys were Thais.
With Rohingya families occupying many of Thailand's shelters, the would-be refugees are the ones most immediately affected by the new rules.
It's not clear at this stage where the teenage boys will be kept as they remain too young to be imprisoned with Rohingya menfolk in police and Immigration cells.
It's also not clear whether Rohingya boys will be removed from their mothers on the day they turn 12 years of age.
Rohingya families appear likely to suffer further hardship not because of something they've done, but because of the failure of Thai authorities in their duty of care.
Having declined to determine the status and future of about 1800 Rohingya who have mostly been held in Thailand since January, the Thai government recently extended its six-month self-imposed deadline for making a decision by another six months.
Frustrated by lack of a decision, many Rohingya women and children have opted to flee the shelters, making them easy prey for the traffickers who continue to operate with impunity along the Andaman coast.
Military and police authorities decline to investigate widespread evidence that renegade officers perform key tasks in the people smuggling industry.