Under new laws introduced at the height of the measles epidemic, schools are not allowed to accept children who have not been immunised.
Parents queued for hours last week to get hold of the immunisation verification documents required from the ministry, with many unhappy that there was a fee imposed at all.
In a statement, the director general of health, Take Naseri, said the fee was wrongly imposed, calling it an outdated practice unauthorised by the ministry.
