Health authorities said they want schools to provide reasons for opting out of an influenza vaccine outreach drive
As the latest seasonal vaccination programme is set to start on September 25, authorities also said jabs have been procured for some family doctors.
Officials said about 23,000 schools, or 99 percent of the city's total, will join the programme.
"Twenty-three schools have indicated that they will not be arranging any vaccination outreach activities, citing reasons such as tight school schedules and insufficient facilities and manpower," said controller of the Centre for Health Protection Edwin Tsui.
"We respect decisions made by the schools... We believe that these schools are facing difficulties as they have stated."
Meanwhile, the government has ordered 100,000 doses of flu jabs for family doctors who joined its vaccination subsidy scheme.
Doctors who obtain vaccines through the administration cannot charge patients additional fees, officials added.
Family doctor Lam Wing-wo told RTHK that the new initiative could prevent over-ordering and insufficient procurement of jabs.
"It would be centrally organised, so that the supply would be more steady. We can just order what we need, after we use up the stocks," Lam said.
More people are made eligible for free or subsidised flu vaccines, such as all chronically ill patients aged 18 to 49, regardless of their financial status.