ALMA operations are carried out by three institutes appointed as Executives on behalf of East Asia, Europe, and North America, in cooperation with the Joint ALMA Observatory in Chile. The East Asia ALMA Support Center, as the main point of contact for East Asian researchers, provides support for the observational studies with ALMA for the East Asian user community, and conducts various activities such as engineering, development, computing, scientific observation support, research promotion, education and public outreach, etc.

As a division of NAOJ, the NAOJ ALMA Project is responsible for operating the East Asia ALMA Support Center as well as coordinating activities in Chile and future planning. NAOJ ALMA Project is located at the NAOJ headquarters in Mitaka and has approximately 90 staff members. After the construction budget of ALMA was approved by the Japanese government, Tetsuo Hasegawa (April 2004 - March 2008), Satoru Iguchi (April 2008 - September 2018), and Alvaro Gonzalez (October 2018 - December 2023) have served as Project Managers.   NAOJ Chile is responsible for the support of NAOJ research activities in Chile, including the support to the operation of ALMA and ASTE telescopes, and the support to NAOJ staff based in Chile. NAOJ Chile has ~10 staff members.   The NAOJ Chile Observatory was established in April 2012. The initial Large Millimeter and Submillimeter Array (LMSA) project office was launched established in 1997 and it has grown into the provisional Japanese ALMA (ALMA-J) project office (from April 2000 to March 2004), and then the ALMA-J project office (from April 2004 to March 2012). The ALMA-J Directors over these periods were assumed by: Masato Ishiguro; Tetsuo Hasegawa; and Ken’ichi Tatematasu. After the establishment of the NAOJ Chile Observatory, the first Director was Tetsuo Hasegawa and the second director was Seiichi Sakamoto. In January 2019, the NAOJ Chile Observatory was divided into the NAOJ Chile and the NAOJ ALMA Project. After the division, the Head of NAOJ Chile was assumed by Shinichiro Asayama, Alvaro Gonzalez (acting), and Tetsuhiro Minamidani. The current Head of NAOJ Chile is Teruyuki Watanabe.