The Teachers Union of Namibia (TUN) cautioned schools may not be ready to reopen in July.
This, it says is due to a lack of adequate resources to ensure social distancing.
The Ministry of Education, Arts and Culture yesterday announced schools will commence face-to-face classes in phases, with Grade 11 and 12 pupils heading back first on 3 June.
Sanet Steenkamp, executive director of education, in a statement said phase two will include preprimary to Grade 3 pupils, who will go back to school on 22 June.
Phase three would see Grades 7 and 9 returning on 6 July, and phase four sends Grades 4, 5, 6, 8 and 10 back on 20 July.
All pupils will end the school year on 18 December.
TUN secretary general Mahongora Kavihuha yesterday cautioned that resuming all classes by the end of July is impractical as there would not be enough time to ensure children's safety.
He said the union proposed conditions for the reopening of schools to the ministry, which include maintaining a distance of one metre between desks, masks provided to each pupil, sanitisers in every class and a hand-washing station at the entrance of each classroom.
"Schools have not received funding for these conditions to be implemented, and we are already in the third week after lockdown. Compromising pupils' health by trying to open in July will not work," he said.
Kavihuha said for pupils to sit one metre apart, additional classrooms and teachers would be required.
Windhoek Afrikaans Privaatskool executive manager Arno van Wyk welcomed the reopening in phases.
He said the school had already desanitised classrooms two weeks ago.
Sanitisers are available in every classroom and thermometer guns have been purchased to take pupils' temperature regularly.
Steenkamp said a mid-term break for teachers is scheduled from 22 to 29 May.
"The ministry of education together with the regional directorates of education, schools, parents, other stakeholders and the community at large will make all the resources at its disposal available to ensure the safety of pupils is prioritised as far as possible," she said.
Steenkamp said the revised school calendar with the ministerial guidelines on the reopening of schools will still be communicated.
All public and private schools closed on 16 March following the confirmation of the first two Covid-19 cases in the country.