As loved ones and school staff looked for Viwe Jali, 5, her body lay in a pit toilet overnight at Luna Primary School.
This was according to Eastern Cape police, who said the little girl is believed to have drowned on Monday. She was only found the next day.
Viwe was reported missing earlier, and her teachers called the police to the school in Bizana when they came across her body, said Captain Edith Mjoko.
She said they were investigating the death as part of an inquest.
"No foul play is suspected. The body is still with the police for a post-mortem."
Jali is understood to have been in Grade R.
Basic Education Minister Angie Motshekga expressed her shock on Thursday upon hearing the news.
"The death of a child in such an undignified manner is completely unacceptable, and incredibly disturbing," she said in a statement.
"I would like to send my sincere condolences to the family of our Viwe Jali, who passed away tragically on Tuesday. I cannot begin to know the trauma the parents are experiencing, it is truly a tragic incident and my sympathies are with them."
Provincial education department spokesperson Loyiso Pulumani said an educational psychologist had been made available to pupils at the school and that a psychologist was also assessing the condition of the teachers.
A third psychologist had been instructed to visit the home of Jali's family to offer support.
The incident was similar to one at a school outside Polokwane on 2014, where 5-year-old Michael Komape drowned in a pit toilet.
His family went to court to claim damages from the State.
The Department of Basic Education said on Thursday that it was doing "everything in its capacity" to address backlogs timeously, by prioritising unsafe structures and those without decent sanitation, electricity and water.
It said it had made significant strides in this regard, together with provincial education departments, but that budget cuts posed a threat to the provision of much needed infrastructure.
"Words cannot express the pain I personally feel at the loss of a young life in this horrific way. To know that, as a sector, we have not been able to address these infrastructure issues fast enough, for a number of reasons, breaks my heart," said Motshekga.
According to the department, 5 225 maintenance projects were underway around the country.
The Eastern Cape has already exhausted its maintenance budget.
The department said that, despite progress made with the accelerated school infrastructure delivery initiatives, more than R3.5bn would be cut in the next three years from the initiative's budget.
The cuts were part of a government-wide reprioritisation of funds, the department explained.