The children were living in a shelter run by the Child Protection Bureau, a government care facility, in Faisalabad district, 100 km from Lahore.
Employees of the Bureau had allegedly subjected them to physical abuse for some time, the officials said.
Taking cognisance of the matter, authorities shifted the children to another government facility in Lahore to keep them in a "safe residence."
Umer Daraz Bhatti, the head of the care facility in Faisalabad, got an FIR registered against nine junior staff members, including attendants, cooks, security guards and a gardener, on charges of sexual assault, physical torture, harassment and forced labour.
The children alleged that the accused used to show them pornographic films and pictures.
They said the accused had threatened them with dire consequences if they told anyone about their actions.
The accused have been booked under various sections of the Pakistan Penal Code though no arrest has been made so far.
Amina Imam, the head of the Child Protection Bureau in Punjab, visited the facility in Faisalabad earlier this week.
After meeting the children, she issued an order for them to be immediately shifted to Lahore.
"I cannot take the risk of keeping the children here as the accused are still at large and they may inflict harm on them," she said.
An employee of the facility told Imam that one of the accused had told him that they were "innocent" as they were being "victimised" by Bhatti for pointing fingers at his alleged corruption.