Education minister Ram Bilas Sharma alleged that there have been lapses on part of the school administration.
"We accept negligence on part of the Ryan International School but the school cannot be derecognised as the future of 1,200 students is at stake," he said.
"We have directed the Gurgaon Police to book the owner of Ryan International School, Albert Pinto, under section 75 of the Juvenile Justice (Care and Punishment) Act, 2015, for cruelty to a child meted out by the custodian in the charge sheet to be submitted in the court within 7 days.
"Some loopholes in the security are visible in the case and the toilet window was also found broken from inside," Mr Sharma told reporters here.
He said the charge sheet in the case will be ready within a week as the police were speedily conducting the probe, but stressed that if the parents of the child insist on a probe by the Central Bureau of Investigation (CBI) or any other agency the government will accede to their demand.
Mr Sharma also made it clear that the school management has to take responsibility for the safety and security of the children.
"We are issuing directives in this regard to all schools including private ones," he said.
"We held a meeting today in which the demand to derecognise the school came up, but we also had to take into account the fact that 1,200 students are studying there. The parents of the students studying in this school were against this step and, therefore, we felt taking such a step will not be right," he said.
"However, for any kind of lapse, by the management or the owner, we have initiated action," he said.
The boy was found murdered with his throat slit in the school washroom in Gurgaon on Friday. The school's acting principal was suspended and the security staff removed. The police claimed the student was killed by school bus conductor Ashok Kumar, who tried to sexually abuse him.
The accused was arrested within hours of the murder after which a court in Gurgaon sent him to police custody for three days.
"The murder accused has already been arrested. Now, within a week, the police after collecting all necessary evidence will submit a charge sheet in court. However, still if the parents are not satisfied, then the Haryana government is ready to get the matter probed by any agency.
"I am hopeful that when we will produce the accused before court within a week with all evidence collected by the police, the parents of the child will be satisfied with the action being taken," he said.
Mr Sharma said, "We have fixed a seven-day deadline in the case where the accused is booked under Section 302 of the Indian Penal Code (for murder). This is the minimum time in such cases. However, if the child's parents still feel they are not satisfied, then as per their wish we can get the case investigated by any agency including the CBI."
"We have full sympathy with the parents of the child. If there is any issue of providing financial help, the Haryana government will be willing to help," he said.
The minister made it clear that the Haryana government will not show any leniency in the matter "Whatever strict action needs to be taken as per the law will be taken in this case," he asserted.
He also said a liquor vend near the school has been ordered to be shut down permanently.