The incident has resulted in a widened food safety investigation into lunch provider Compass.
Ilminster Intermediate School principal Jonathan Poole, told Morning Report, his understanding was a student went to grab his lunch, a cottage pie in a plastic container, and was carrying it to his table when he realised it was too hot to hold and dropped the meal.
Poole said it splattered over the boy's legs and resulted in him needing treatment at Gisborne Hospital for second degree burns.
"It's not something you'd expect to happen - my understanding is the lunches are meant to be heated at a certain temperature, delivered and then eaten at a certain temperature."
Following the incident, Poole said he spoke with ministry officials and Associate Education Minister David Seymour, called him to pass on his apologies.
"I spoke to him and passed on my concerns about the entire lunch programme.
"They were very apologetic - their intention is not to burn children, but yesterday, the meals were far too hot.
Poole suggested a regional approach was needed for schools.
"For context, my school is 10 minutes away from the heating facilities, so the distance for them to cool down is not far."
Poole said in the past the school used a local provider for their lunches that worked well for them.
"The meals were good, daily and consistent - now, this system is more miss than hit."
The School Lunch Collective's spokesperson Paul Harvey, who was also the director of the Compass Group, said in a statement on Thursday, 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," he said.
Harvey said they have started an investigation, and have removed the meal involved in the incident from the menu, until the investigation has been completed.
The Ministry of Education's leader of operations and integration Sean Teddy 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," he said.
Teddy said a full investigation would be undertaken.
"We extend our sincere apologies to the student and their family for what has occurred," he said.
"At the request of the Ministry of Education, we will also widen our investigation to heating facilities used by the school lunch programme nationwide to provide assurances their practices are fit for purpose," MPI said in a statement.
Associate Education Minister David Seymour said in a statement he was "deeply concerned" by the incident.
There has been a string of complaints from schools about the revamped scheme including late delivery of lunches, repetitive menus and plastic melting into the contents.
Heat of lunches 'challenging'
The principal of Haeata Community Campus in Christchurch, Peggy Burrows, told Morning Report, her school was also finding the heat of the meals "challenging".
"Our school has children from 5 up to 18 and it's hard for our young ones to open up these hot containers.
"We were promised they would be in a ready to eat tray and that's just not happening. They arrive in aluminium punnets and they must be really really heated, because steam comes out when we open those carriers."
The steam was "very hot", Burrows said, but no children had been badly burnt.
"There are little finger burns, but nothing like what happened in Gisborne."
She said teachers were using cloths to make sure the food was covered and students were not left by themselves now to open the lunches.
Compass Group has been approached for comment on Burrow's comments.
