The Ministry of Health says the high rate of sickness at schools is unrelated to meningococcal B vaccination.
Schools in some areas, especially Auckland and Wellington, have reported that up to a quarter of their pupils are away sick.
The children are mainly suffering from coughs and other respiratory symptoms, but some have had diarrhoea and vomiting. Public health authorities say a flu outbreak is probably the main cause, although some Wellington school pupils have also had norovirus, a stomach bug.
The Immunisation Awareness Society's principal researcher, Sue Claridge, said yesterday that injections of meningococcal B vaccine had just been given in some Auckland schools.
"We have had some reports that suggest there are high levels of absenteeism as a result of that. When vaccination coincides with the beginning of the cold and flu season you would expect to see quite high rates of absenteeism. We believe all vaccines place a strain on the immune system."
But a ministry public health physician, Dr Kerry Sexton, said the flu outbreak was not linked to the vaccinations.
"There's no international evidence to support that this vaccination with MeNZB, [the meningococcal B vaccine] or any other vaccine, puts people at increased chance of getting the flu. It's just that it's the influenza season at the moment ...
"It's just coincidence that some people have been vaccinated and may have gone on to get the flu."
"There's no evidence to show that vaccination will reduce the body's ability to fight infections. When you've got influenza, your immune system is heightened."
Having a mild illness was not a valid medical reason for avoiding vaccination, she said. The only "contra-indications" were having a fever or a history of severe allergy to any component of the vaccine.
The vaccination programme would not be postponed; the aim was to complete it as quickly as possible, to protect the recipients from meningococcal disease.
Two Auckland schools yesterday said their high rates of absences started before their second round of injections.
Gladstone Primary's deputy principal, Judd McLauchlan, said between 60 and 80 of the school's 900 pupils had been away every day since last Tuesday. The second dose of vaccination occurred on Thursday and Friday.
At Pt Chevalier School, where the injections were given yesterday - six weeks after the first dose - 120 of the roll of 585 were absent; last Thursday 100 were away. The principal, Sandra Aitken, said this was the third week of high absences.
The three-jab vaccination programme, which started in Auckland last July, began in Otago and Southland yesterday and will move up the South Island. Some 350,000 of the target 1.1 million under-20-year-olds have so far received at least one dose.
An independent safety monitoring board set up by the Health Research Council said in February that it had no concerns about the vaccine's safety.
Trials before the vaccine programme began found that common side effects included fever, vomiting and diarrhoea in young children, and headache and general malaise in adults and children.