Face-to-face learning for Grade 11 and 12 pupils started at Walvis Bay on Monday, after they had to stay home for about four months.
There were mixed feelings from parents, teachers and pupils about the resumption of face-to-face classes, though.
Some teachers said they had no choice but to start teaching, although Walvis Bay has become Namibia's novel coronavirus pandemic epicentre.
Teachers said they feared returning home to their families every day, as they do not know which pupils or colleagues could be carrying the virus.
Some parents allowed their children to return to school on Monday, fearing they would have to repeat the year if they do not go to school, while others opted to collect learning materials from schools, in order to protect their families.
Most of the high schools at the town had more than 50% attendance.
"We sent out some letters to learners that are still outside the regions who want to come back. They will be allowed to return to Walvis Bay," said Flamingo Primary School teacher Theresia Goagoses. "We will see how it goes. We are trying to keep safe and educate the learners about safety as best as possible."
"Some parents are at ease after we communicated all safety measures to them. Others are worried about their children, and we will have study material for them to collect. We are eager to teach and will see how it goes," said Duinesig Combined School principal Stanley Urikhob.
"I don't know why we cannot get the situation in Walvis Bay under control first," parent Dina Shigwedha said. "One learner can infect an entire school and family at home. My child will stay home."
One of the schools sent back ten learners who indicated through questionnaires that they had been in an environment where people tested positive or were showing flu symptoms. They will return to school after testing.
Some schools say they are not ready for Grade 10 pupils on Tuesday, as they are many and it will be a challenge to adhere to social distancing.
Ablution facilities at some schools are also not fit for a large group of pupils.