Family doctors have stopped using a brand of flu vaccine connected to convulsions suffered by four children under the age of five.
The Ministry of Health has told GPs not to use Fluvax after the children had fits caused by a high fever, known as febrile convulsions.
Fluvax can still be given to adults, but children will be immunised only with Vaxigrip and Influvac.
The ministry says convulsions are rare and would usually happen within 24 hours after vaccination.
The Medical Association says parents should be reassured doctors will not use the vaccine linked to the bad reaction.
On Thursday, Western Australia temporarily suspended a free influenza vaccination programme for children under the age of five after similar reactions.