In a statement,Ms Farmer said she had contacted Attorney-General Yvette D'Ath to ensure the investigation would begin"as quickly as possible".
"I know the community wants answers about these two horrific incidents,and so do I,"she said.
"There is absolutely no excuse for the neglect of children in our community."
The investigation will be carried out by Commissioner Cheryl Vardon and take place"completely at arms length"from the government.
The independent investigation into both incidents comes less than two months after adamning review of the department's complaint system by Queensland Ombudsman Phil Clarke that identified issues including misclassification and under-reporting.
The report also declared the complaint system was"unnecessarily complex and confusing"and leads to"frustration and delay".
It followedearlier calls for an overhaul of the system from the coroner and auditor-general.