The top court's notice came after a PIL was filed by an NGO, Manav Adhikaar Nigraani, and an advocate Sanjeeb Panigrahi.
The petitioners argued that the recent deaths in Bihar, Odisha and West Bengal show that there was no effective monitoring and evaluation of quality of food served to students under the scheme.
"In over 12 lakh government-run and aided schools, children receive free, cooked lunch every day but they are constantly exposed to risk of food poisoning and other related health hazards due to lack of infrastructure and proper monitoring of the scheme," the petitioners said.
The petitioners also wanted criminal action those responsible for the death of the children.
"Lack of cleanliness occasionally leads to food poisoning, Children fall sick and there is a backlash against the whole programme from parents and teachers. This is actually not difficult to avoid, but it requires paying close attention to safety and hygiene at all times. The cook and helper have a special responsibility in this respect. Anyone who is involved in the cooking process should maintain strict personal hygiene and other safety measures," Mr Panigrahi said.
The Centre and the States of Bihar, Odisha, West Bengal, Assam, Uttarakhand, Uttar Pradesh, Chhattisgarh, Madhya Pradesh, Tamil Nadu, Kerala, Karnataka and Jharkhand will have to reply to the Supreme Court in four weeks.