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.

After the construction budget of ALMA was approved by the Japanese government, the East Asian ALMA Project Manager was assumed by Tetsuo Hasegawa (April 2004 - March 2008) and Satoru Iguchi (April 2008 - September 2018). The current Project Manager is Alvaro Gonzalez.

As a division of NAOJ, the NAOJ ALMA Project is responsible for operating the East Asia ALMA Support Center as well as coordination of activities in Chile, future planning, and budget request. NAOJ ALMA Project is located at the NAOJ headquarters in Mitaka. NAOJ ALMA Project has ~80 staff members.

NAOJ Chile is responsible for the management of NAOJ research activities in Chile. NAOJ Chile manages NAOJ researchers staying in the Joint ALMA Observatory and is responsible for smooth operation of ALMA. NAOJ Chile is also responsible for the operation of ASTE. NAOJ Chile has ~20 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 this division, the Head of NAOJ Chile was assumed by Shin'ichiro Asayama.