Basic Education Minister Angie Motshekga on Thursday committed to abide by the Presidency's instructions for an audit of school sanitation facilities within three months.

She was addressing the media after calling all education MECs, education department heads and infrastructure officials to attend an urgent Council of Education Ministers (CEM) meeting in Kempton Park, Gauteng earlier in the day.

The nation reacted with horror when five-year-old Lumka Mketwa drowned in a pit toilet at Luna Primary School in Bizana in the Eastern Cape, more than a week ago.

Motshekga said the loss of an innocent young child was a "truly painful experience" and had once again drawn their attention to ongoing sanitation challenges.

The "current crisis" necessitated a meeting to reflect on the plans already in place and what more could be done.

"After the discussion I had with the president last week, we did commit our department to provide a detailed audit of sanitation facilities with costed emergency plans and timelines to address these challenges," she said at the briefing in Johannesburg.

Information they already had just needed to be verified and she anticipated it would take less than three months.

The audit and costed plan would look at what was still outstanding and could be fast-tracked, she added.

Some schools in the Eastern Cape, which have no sanitation at all, would be addressed with urgency.

Motshekga said one of their biggest challenges, which affected half of their schools, was that old pit toilets remained on site despite the construction of alternative ablution facilities.

The audit would include the schools which needed to have these pit toilets demolished.

Other schools had inadequate sanitation, especially in Gauteng where overcrowding was being experienced.

Where schools had Grade R pupils, the audit should establish if there were toilets that are fit for smaller pupils.

Existing facilities may be refitted with age-appropriate toilet seats.

The Treasury would need to approve any deviations from existing budgets.

Motshekga said they would work with the SA Police Service to establish the circumstances leading to Mketwa's death.

"The father has his views about what would have happened. In all fairness, we will need to get to the bottom [of it] so we are all satisfied," she said, adding that they have to wait on a full investigation instead of relying on "hearsay".

The SA Human Rights Commission said last week that it had launched its own investigation into the incident.

It has not yet responded to a request for comment on the progress of its probe.