The UN health agency warned on Tuesday that progress in fighting malaria is threatened by the emergence of a drug resistant strain and defiance of its advice on crucial new medication.
In a report, the World Health Organisation also pinpointed insecticide- resistant mosquitoes as another "major threat" to attempts to drastically cut and ultimately eradicate the mosquito-borne parasitic disease.
The WHO's annual snapshot of efforts to tackle malaria, which affected 243 million people in 2008, showed that the caseload had fallen by about two percent in two years while the global death toll declined by a similar amount to 843,000.
More than one third of the 108 affected countries have managed to cut their malaria cases by more than 50 percent since 2000.
The "2009 World Malaria Report" credited growing use of insecticide treated bednets for much of the progress in recent years, especially in some of the African nations that shoulder 89 percent of the global burden of the mosquito borne disase.
However, experts including a maker of impregnated bednets, warned last week of a rise in insecticide resistant mosquitoes in Nigeria, where about 300,000 people die each year from the disease.
The WHO also highlighted the slow take up of Artemisinin-based Combination drug Therapy (ACT) in most African countries.
The new Artemisinin-based drugs - which were developed largely because older antimalarials became ineffective as the parasite developed resistance to them - are meant to be used as a combination therapy with another drug.
Instead, the WHO found that 37 nations, mainly in Africa, as well as in the Americas and southeast Asia, were still using Artemisinin alone, despite a 2007 WHO assembly resolution calling for "strong action" against monotherapy.
"Continued use of artemisinin monotherapy is a major factor in parasite resistance," the report said.
"Parasite resistance to antimalarial medicines and mosquito resistance to insecticides are major threats to achieving global malaria control," it warned.
The WHO reiterated a request it made to pharmaceutical companies three years ago to stop producing an marketing monotherapy drugs.
By the end of 2008, 12 out of 68 had complied while 22 more had declared their intention to halt production, according to the WHO.
"As the private sector pharmaceutical markets in many malaria endemic countries are unregulated, pharmaceutical companies tend to ignore the WHO guidelines," the report said.
The UN health agency said earlier this year that it was fighting emergence of new Artemisinin resistant malaria on the Thai-Cambodia border.
Strains of malaria resistant to previously common antimalarial drugs such as mefloquine also emerged for the first time there and later spread into Africa.