The disease, which is carried by parasite-bearing mosquitoes, kills around 650,000 people each year, mostly African children under five, according to the UN's World Health Organisation (WHO).
While there are a number of preventative medicines already in use, scientists say drug-resistance is growing.
Researchers from Osaka University have developed a dry powder vaccine, called BK-SE36, from a genetically-modified protein found inside the parasite, which they mixed with aluminum hydroxyl gel.
"The vaccine's effect is greater than those hitherto reported of any other antimalaria vaccines," a statement issued this week said, adding BK-SE36 is expected to reduce markedly the number of deaths caused by the mosquito-borne disease.
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A follow-up study of people in Uganda, aged between six and 20, found the vaccine lowered the number of people infected by malaria by 72 per cent.
The findings were published on Tuesday on the online US science journal PLOS One, according the statement.
BK-SE36 far outperformed the 31 per cent decline achieved by another new vaccine developed by a British company, the statement said.
Professor Toshihiro Horii, who led the study, told Jiji Press he wants to put BK-SE36 to practical use "in five years after conducting a clinical trial on infants between zero and five, who account for the bulk of malaria deaths."
The Global Health Innovative Technology Fund (GHIT Fund), set up by the Japanese government, Japanese pharma companies and the Bill & Melinda Gates Foundation, said they were looking at a potential five-year commitment of more than USD 100 million to support research and development into neglected diseases.
The project will see researchers looking through the libraries of compounds held by drug companies to see what possible treatments they contain for tuberculosis, malaria, and other illnesses that threaten hundreds of millions of people in the developing world.