The programme has come under fire after numerous problems were reported by schools recently, including plastic melted into the food.
New Zealand Food Safety said it was notified late this afternoon of the serious incident.
"We immediately started an investigation and we will be onsite at the lunch heating facility tomorrow," deputy director general Vincent Arbuckle said.
The lunch was heated at an offsite facility, not at the school, he said.
Ilminster Intermediate School's principal told Stuff that the student was burned when the lunch spilled onto their leg.
"It was too hot, it dropped, it exploded and splattered all over his leg and basically gave him second-degree burns," Stuff reported the principal as saying.
The student was reportedly treated at a local hospital.
Arbuckle said they would be investigating at the facility tomorrow.
He said they were in contact with the Ministry of Education and the Compass Group - one of the three companies that make up the School Lunch Collective responsible for running the scheme.
Arbuckle said all food businesses were required to identify potential risks and have plans in place to manage the risks.
"The safety of the students is our primary concern. We will be investigating to determine what went wrong in this case and to help prevent it from happening again."
The School Lunch Collective's spokesperson, Paul Harvey, who is also the director of the Compass Group, said in a statement the incident was "deeply regrettable".
"Our thoughts are with the student, and we wish them a speedy recovery. We take health and safety seriously and are talking to the school to see how we can support both them and the student."
An investigation has begun and the meal involved in the incident taken off the menu in the meantime, he said.
Sean Teddy, the Ministry of Education's leader of operations and integration, said the incident "should not have happened".
"The Ministry is very troubled to learn a student has been hurt as a result of a hot meal spilling out from its packaging and burning their leg."
Teddy said a full investigation would be carried out.
"We extend our sincere apologies to the student and their family for what has occurred."
Associate Education Minister David Seymour said in a statement he was aware of the incident.
"I am deeply concerned and I want to extend my sympathy to the child who has been injured."
There has been a string of complaints from schools about the revamped scheme including late delivery of lunches, repetitive menus and huge wastage.
