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Indonesian universities are not producing sufficient number of world-renowned international researches or publications. This is reflected by the number of quoted international scientific articles, which even falls under Bangladesh, Kenya, and Nigeria. This is concerning, because countries with fewer higher education institutions such as Singapore, Malaysia, and Thailand, are able to produce more international publications. With that fact in mind, this research is aimed to explore research challenges at four universities in Indonesia (University of Indonesia, University of Gadjah Mada, Catholic University of Atma Jaya, State Islamic University (UIN) Syarif Hidayatullah).