A meningococcal outbreak mainly affecting Aboriginal children from Central Australian communities could spread to the Top End, NT health experts say.

Northern Territory health authorities have mounted a large-scale immunisation campaign in an attempt to prevent an unprecedented Central Australian meningococcal outbreak from spreading to the Top End.

There have been 18 confirmed cases of the deadly disease so far this year, mainly in Aboriginal children from Central Australian, Barkly and Katherine communities.

There were only three cases in 2016, according to the NT Centre for Disease Control.

The majority of the cases are children aged under 10 infected with the serogroup W, a strain that has risen rapidly with at least 10 cases detected in September alone.

"It's unprecedented, and nationally this serogroup has emerged as a real problem," CDC acting director Charles Douglas said.

The government will this week begin offering free vaccinations to Aboriginal people aged between 12 months and 19 years in affected regions and remote communities.

Dr Douglas says the measures may not contain the outbreak, and there are plans to roll out the vaccination program to all one-year-old kids Territory-wide by early 2018.

He said indigenous people were more susceptible to the W strain due to the high mobility of Red Centre communities and the overcrowded conditions in which they live.

"It's a very hard germ to catch - you've got to be in close contact with someone for quite a long time," he said.

WHAT IS MENINGOCOCCAL?

* A rare, life-threatening illness caused by bacterial infection of the blood and/or the membranes that line the spinal cord and brain and occasionally infect other sites, such as large joints.

WHAT ARE THE SYMPTOMS?

* Fever, a stiff neck, severe headache, confusion, difficulty looking at bright lights, vomiting, sore muscles or joints, drowsiness or a rash.

HOW IS IT TREATED?

* With antibiotics, but the infection can progress very quickly, so seeking medical attention urgently is vital to survival.