At the campaign launch Ms Deacon said: "I am delighted that so many parents and young people in Scotland have responded so positively to the meningitis C immunisation campaign.
Health Minister Susan Deacon said advertisements would be placed in weekend newspapers urging the parents of unvaccinated youngsters to contact their family doctor.
The "mop up" campaign is intended to ensure that young people who missed the autumn round of vaccination receive immunisation jabs.
All schoolchildren and students under 18, in Scotland, have been offered vaccination in an effort to reduce the number of cases of meningitis C, the most fatal form of the infection.
At the campaign launch Ms Deacon said: "I am delighted that so many parents and young people in Scotland have responded so positively to the meningitis C immunisation campaign.
"The vast majority of Scottish children and young people are now protected against this very serious infection, I have no doubt that it has saved and will continue to save many young lives.
"But we cannot be complacent. Although provisional uptake figures are very encouraging, we now want to ensure that as many young people as possible get protection against this frightening disease.
"I am today urging young people under 18 years of age and the parents of children who have missed out for any reason to contact their GP as soon as possible to arrange for immunisation."
Deaths avoided
Official figures reveal that in the last six months there was a 90% drop in cases among babies under one-year-old and in the 15-17-year-old age group.
It is estimated that 500 cases of Group C meningococcal meningitis and septicaemia have been prevented since the start of the UK-wide vaccination programme and 50 deaths have been avoided.
But a leading Scottish health charity says more must be done to combat other forms of the disease.
The Meningitis Association of Scotland insists a vaccine must also be developed for meningitis B, which accounted for more than half of the 327 meningitis cases in Scotland last year.
British scientists are currently studying a prototype meningitis B vaccine that has been developed by experts in the Netherlands.