Education minister Christine Choi said on Saturday that students with amber codes should go to school only if the campus environment is suitable.
Under the new quarantine rules, which came into effect on Friday, inbound travellers will receive an amber health code during a four-day medical surveillance period after spending three nights in hotel quarantine. With the amber code, people are barred from entering "high-risk" premises, such as restaurants, but are still allowed to go to work or school.
Speaking to reporters after a ceremony, the education chief said it was up to schools to make appropriate arrangements for students who have the amber code.
"If these students have full-day classes and it's a must for them to have lunch on campus, they should be partitioned and eat separately. The places where they eat should be cleaned thoroughly. Schools should consider the campus environment and their own situation before arranging for students with the yellow codes to return to school," she said.
She added that schools had the responsibility to make sure students declare their red or amber code status and meet the requirements for going to school.
Earlier, the Education Bureau issued guidelines, saying students and staff with the amber codes shouldn't take part in mask-off activities and should take daily rapid tests.