The SA Human Rights Commission has written to Basic Education Minister Angie Motshekga to recommend that she delay the return to school of Grade 7 and 12 pupils.
They are set to return on 1 June but according to the commission, the Northern Cape office had indicated schools in that province would only be ready by 8 June.
It added various teachers' unions also said the required conditions have not been met.
According to school governing bodies, about 3 500 schools did not have enough water.
"All these reports give the commission concerns whether - and considering that only three days remain before the date of opening as well as the amount of work that appears still remaining to be done - the schools will be ready to receive learners with the expected levels of safety by 1 June 2020," it stated.
"The commission has therefore communicated its concerns by letter to the minister and recommended that she reconsider the date for reopening the schools."
The commission was also worried about pupils who do not have data or the technology for distance learning.
Teachers have started going back to school to get used to the new conditions from 1 June, which include setting out wider spacing between desks, taping distancing marks on corridor floors, and receiving sanitisation packs.
Motshekga has toured some schools to inspect the extra water tanks brought in, and has anticipated that the first few days from 1 June are bound to be spent on settling in to the new way of schooling until Covid-19 risks have dissipated.
- Compiled by Jenni Evans