The World Health Organisation says Malawi has become the first country to begin immunising children against malaria, using the only licensed vaccine to protect against the mosquito-spread disease.

Although the vaccine only protects about one-third of children who are immunised, those who get the shots are likely to have less severe cases of malaria.

The parasitic disease kills about 435,000 people every year, the majority of them children under five in Africa.

“It’s an imperfect vaccine but it still has the potential to save tens of thousands of lives,” said Alister Craig, dean of biological sciences at the Liverpool School of Tropical Medicine, who is not linked to WHO or vaccine.

Professor Craig said immunising the most vulnerable children during peak malaria seasons could spare many thousands from falling ill or even dying.

The vaccine, known as Mosquirix, was developed by GlaxoSmithKline and was approved by the European Medicines Agency in 2015.

A previous trial showed the vaccine was about 30 per cent effective in children who got four doses, but that protection waned over time. Reported side effects include pain, fever and convulsions.

Mothers prepare to have their children vaccinated. Photo: Getty

Dr Pedro Alonso, director of WHO’s malaria program, said similar vaccination programs would begin in coming weeks in Kenya and Ghana, with the aim of reaching about 360,000 children a year across the three countries.

Dr Alonso called the vaccination rollout a “historical moment”, noting that it was significantly more difficult to design a vaccine against a parasite as opposed to a bacterium or virus.

He acknowledged the vaccine was flawed but said the world could not afford to wait for a better option. “We don’t know how long it will take to develop the next-generation vaccine,” he said. “It may be many, many years away.”

Resistance is growing to medicines that treat the disease, while mosquitoes are becoming more resistant to insecticides. In addition, funding for malaria efforts has plateaued in recent years.

It took GSK and partners more than 30 years to develop the vaccine, at a cost of about $US1 billion. GSK is donating up to 10 million vaccine doses in the current vaccination initiatives.

“This malaria vaccine is going to save many lives, even if it is not as good as we would like,” Professor Craig said. “But I hope this will kick-start other research efforts so that the story doesn’t end here.”

-AAP