A committee of senior officials will investigate the case, N C Joshi, a spokesman for the women and child welfare ministry, said on Wednesday.
The discovery of skeletons last week sent shockwaves across the country and triggered a public uproar, prompting the government to act.
The committee is supposed to submit its report in 15 days, Joshi said.
The skeletons were found in a drain next to a house in the Delhi suburb of Noida.
The owner of the house, Moninder Singh Pandher, and his domestic servant, Surender Kohli, have been arrested and charged with kidnapping, raping and killing the victims and then dumping their dismembered bodies in the drains.
Police say Kohli confessed to killing the children when confronted with photographs during questioning.
Growing anger
Relatives of the victims say the police had been apathetic and refused to entertain their complaints when the children went missing.
"They said my daughter was pretty and immoral and must have run away," Jatin, the father of a young girl who went missing, told the NDTV television channel.
Gopal Haldar, whose daughter Bina is missing, said that the police refused to register his complaint.
The police reportedly refused to listen to them since they are very poor and therefore without a voice.