Ambulance NSW says paramedics and the CareFlight helicopter were deployed to Manly West Public School at Balgowlah, on Monday afternoon, responding to 12 patients with burns.
Eleven students from year 5, believed to be aged around 10, were treated at the scene before being taken to various hospitals.
All of the children are in a stable condition, however two suffered serious burns and were transported to hospital under the care of specialist medical teams.
Nine other children suffered superficial burns and were also taken to hospital for treatment.
The two children with serious burns were taken to Westmead Children's Hospital, five children are being treated at RNS Hospital and four are at Northern Beaches Hospital.
An adult who also received superficial burns was taken to Northern Beaches Hospital in a stable condition.
The students were conducting an outdoor science experiment, mixing sodium bicarbonate and methylated spirits.
NSW Ambulance Acting Superintendent Phil Templeman said the experiment was affected by high winds which blew some of the materials around.
"The children have sustained burns to the upper body, chest, face and legs," he said.
"Thankfully, the majority of the students were not badly injured."
Police officers initially responded to what was labelled a HAZMAT incident shortly after 1pm on Monday.
Concerned parents gathered outside the school gates for news, surrounded by ambulances and police vehicles.
NSW Education Minister Sarah Mitchell said her department would provide whatever resources the school and community needed in coming days, including counselling.
"I want to particularly thank and acknowledge all of the school staff who acted so quickly to provide first aid and call emergency services," she said in a statement.
The minister said her department, NSW Police and Safework NSW would carry out their own investigations into the incident.
State MP for Manly, James Griffin offered the school help, saying he knew the staff and the students "very well".
"My thoughts go out to all of them," he tweeted.
