Only pupils with underlying health conditions that make them more at risk to flu will continue to receive the Fluenz Tetra nasal spray as scheduled.
It comes after the vaccine programme for Fife school children was postponed last week.
Health bosses have apologised for the delay, which has been caused by batches of the spray failing quality assurance tests.
NHS services have been told to focus limited supplies on two-to-five-year-olds not yet in school and school pupils with existing health problems.
A letter to health service leaders last week said supplies could be delayed by a month. The adult flu vaccine programme is not affected.
NHS Grampian said:
“We are currently working to find alternative ways in which we can make vaccinations available to pupils whose inoculation has been postponed, once the supply of vaccine resumes. We will advise these arrangements to schools and parents as soon as possible.
“We apologise for any inconvenience this may cause to parents, pupils and primary school staff.
“We would advise parents that GP practices will only vaccinate those children aged 2-5 years old or those children aged 5-18 with an underlying health condition.”