Malaria in Indonesia is concentrated on the outer islands of Papua, Maluku, Nusa Tenggara, Sulawesi, Kalimantan, and Sumatra. It occurs with low frequency or is absent on the islands of Java and Bali where approximately 70% of the population live. All species of human malaria were found in Indonesia. Formerly, P. malariae and P. ovale were mostly found in the eastern part of Indonesia, Nusa Tenggara Timur and Papua. However, in recent years, both species has been detected in Lampung Province and in the island of Nias, respectively. Vivax malaria was apparently more predominant in Java whereas in the outer islands the prevalence of vivax and falciparum malaria was equal.

During pre eradication era, the malaria situation in Indonesia was as bad, if not worse, as in India. The estimated malaria cases and deaths were around 30 million (in Java and Bali only) and 0.12 million respectively annually. But due to result of progress in eradication programme, the island of Java and Bali was practically malaria free by 1964. From 1965, the situation began to deteriorate the malaria incidence gradually increased and disease spread over the islands. In 1968, the malaria eradication services extended to areas of social-economic areas in other islands.

The number of reported cases increased form 10,011 in 1965 to 117,056 in 1970 and 346,233 and 229,693 in 1973 and 1974 respectively following an outbreak in Java and Bali. Thereafter, there was a continuous decline in reported cases which reached up to 78,854 in 1979. This reduction of malaria incidence was attributed partly to better timing of spray and improvement in treatment. From 1990 onwards, The malaria situation continued to improve and reported case static around 20,000 per annum and it reached to its lowest recorded cases at 7089 in 1995. After that, situation deteriorated unabated until 2000. The reported cases doubled in 1996 as compared to 1995, in 1998, it multiplied by more than two folds as compared to 1996 and further in 2000, the reported cases doubled than 1999 and reached to 101852. There after situation starts improving again and in 2004, the reported cases were 7,774. There was an increase in the number of recorded cases from 268,000 in 2001 to 411,797 in 2008. The Pf proportion was static around 45-50%. The increase in confirmed malaria cases are most likely due to an increased focus on diagnosis and treatment of cases in Eastern Indonesia as a result of new investments in malaria control. The ABER in 2008 for Indonesia was 1.3% but was highest in West Papua (Barat) 14%, Papua 10%, Maluku 6.2%, Nusa Tengarah Tengah 5.8%, provinces in Eastern Indonesia with known high endemicity. 2.15 million LLINs were distributed between 2004 and 2008, enough to cover 6 million population living at high risk of malaria. The IRS activity in the country was very limited and almost negligible.

Most of the control programme has been carried out in Java-Bali. The residual foci are in Central Java. Drug resistance to P.falciparum is a problem and has been identified in all 30 provinces : at RIII level in 4 provinces, and at RI-RII levels in 26 provinces. Low to moderate level of resistance also noticed for SP compound as well as Mefloquine in Irian Jaya. P.vivax resistance to chroroquine was first reported in 1991 from Irian jaya province. At present, country has adopted ACT for treatment of both types of malaria species.