The government said that, although it is close to containing the problem, some students must wait until health standards are improved at their schools.
Many schools in Zambia reopened this week after the outbreak of cholera that infected more than 3600 people and killed 78.
But some will stay shut for at least another two weeks until the education ministry is satisfied over their hygiene and sanitation standards.
"We wish to advise parents and community members in the affected areas to cooperate with the government's directive so that we focus on saving lives," said Nondo Chilonga of the Ministry of General Education.
She said schools in three of the six operational zones in the Zambian capital Lusaka will remain closed.
Chilonga said: "All the schools in these areas are not opening whether they were initially cleared or not by the Ministry of Health."
The start of the school year was postponed by the cholera outbreak, which began in October.
It had been announced that schools would stay shut until the end of January - then that was changed to January 21.
The government said on January 23 it is close to containing the outbreak, adding that cases have dropped from an average of 164 a day to 25 to 30. But in Eastern Province, Permanent Secretary Chanda Kasolo said several would stay closed due to poor sanitation.
Kitwe District Commissioner Binwell Mpundu said 10 of the 36 schools that were inspected did not meet the recommended health standards.