The use of true shallot seed (TSS) has been promoted as an alternative method to obtain healthy and high quality shallot seed that supposed to be adequately available for farmers along the year. The use of TSS is expected to be able of solving quantity and quality problems of shallot table consumption and shallot seed in Indonesia. A functioning institutional setting should be established in line with the development of TSS. The establisment of good and strong institutional could generate innovative appropriate technologies and ensure the availability of TSS in a long term. The objective of this study was to investigate the stakeholders' choice of some institutional models to support the development of TSS shallot seed system in East Java. A survey was conducted from March to August 2016 to collect data by interviewing 35 respondents. Data were analysed by employing the Analytical Hierarchy Process (AHP) concept and using Super Decisions statistical program. Results indicates that an institutional setting selected by respondents to support the development of TSS shallot seed system in East Java is described in the first option. The first option suggests that Indonesian Vegetables Research Institute (IVEGRI) and Assessment Institute for Agricultural Technology (AIAT) have the role of producing TSS for Breeder Seed class (BS) from high quality shallot bulbs and providing legality delegation or license to BBI/BBU/BBH (Indonesian government seed institutions)/Private in producing/multiplying seed bulbs of BS class. Afterward, the University/AIAT/Private will produce TSS and seed bulbs for Foundation Seed class (FS). Furthermore, selected shallot seed growers will produce TSS and seed bulbs for Stock Seed class (SS) and Extension Seed class (ES). The ES will be used by farmers to produce shallot bulbs for table consumption. Production of FS-TSS, FS-seed bulbs, ES-TSS, and ES-seed bulbs will be monitored and supervised by AIAT.