Malaria cases in Aru Islands district is remain high in 2013, shown by high number of clinical malaria patients (1.617 person), 620 person were laboratory confirmed, 14 of them was pregnant women. This study was aimed to assess the condition of the public health center (Puskesmas) in order to eliminate malaria in Indonesia by 2030. Study was a documents observation and in-depth interviews in charge of malaria and other relevant officials in the District Health Office (DHO) in October 2014. Study was designed by cross sectional. Information on human resources (HR), facilities and budgets and territorial obtained by questionnaire tool prepared for mentoring troubled areas of health (PDBK) 2014. The results shown that both morbidity and suspected malaria evenly in each Puskesmas. Malaria control program in the form of distribution of mosquito nets and RDTs examination in Puskesmas were already done. Theworkers who handle malaria were not distributed well, even for health analysts were still lacking. Facilities were concentrated in Dobo Puskesmas and public hospitals. This study recommends the need of microscopic health analyst as well as research to improve the report system and evaluation of the effectiveness of the mosquito net USAge.