Twenty Hoërskool Driehoek pupils remain hospitalised in Vanderbijlpark and other parts of Gauteng.
The teenagers sustained severe injuries which could result in some of them facing the prospect of amputation, sources close to the incident have told News24.
Roydon Olckers, Jandré Steyn and Marli Currie lost their lives in the tragedy at the school on Friday. In total, 23 others were taken to various hospitals in the area.
On Friday morning, a concrete slab above a corridor linking two blocks of buildings came crushing down on 26 learners. The incident happened few minutes after 8:00, when learners were heading to their classrooms from the morning assembly.
Gauteng Education Deaprtment head Edward Mosuwe said he could not reveal the state of the injuries the learners had suffered. Instead, he said people should give the medical practitioners space to perform their job.
Vaal Weekblad reported that at least three children were critically injured and several prayer groups have been created for them, as well as for the others who were affected.
Netwerk24 reported that Shamone Steynvaart, who is in Grade 9, suffered severe injuries and doctors were fighting to save her from paralysis in her lower body. Marnus Nel needed the arteries sending blood to his legs restored, Netwerk24 reported.
Three learners have since been discharged from hospital, Mosuwe confirmed.
"I can confirm that three deceased learners have been positively identified. MEC Panyaza Lesufi and the school are continuing visiting learners who are in hospitals," he said.
The school remain closed on Saturday and has been taken over by the Department of Labour and police as they conduct separate investigations into what caused the structure to collapse.
Structural engineers who have been on the ground since Friday have erected scaffolding below the triple story blocks of the school.
Plastered cracks below the first floor were visibly clear which could have forced engineers to balance the buildings from collapsing further.
"The school remains cordoned off by police as they are investigating what caused the tragedy. The school has been declared an emergency area. Structural engineers are on the scene. As the department, we want to know what caused the accident," Mosuwe said.
The head of department thanked all who played a role in assisting with the removal of pupils trapped under the rubble.
The department has offered trauma counselling services to all affected individuals.
"Until we have dealt with trauma counselling then we will deal with the recovery process. We have found an alternative place on the school grounds to manage teaching and learning.
Mosuwe added: "We have received overwhelming support since Friday. Regarding access to the school, the department of education will be guided by the department of labour."
The department has promised to give deceased learners a proper and dignified burial.
Mosuwe said the department had not received complaints about the school's infrastructure.
However Vanderbijlpark police head, Brigadier Nikiwe Hoyana, promised that should foul play be found, police will not hesitate to act against the culprits.