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| footer = Heri Oktavian (kiri) dan Harry Setyawan (kanan), dua komandan kapal selam yang hilang kontak
}}
* [[Mayor|Mayor Laut]] (P) [[Muhammad Ali (militer)|Muhammad Ali]] (2004-20062004–2006<ref>{{Cite web|date=18 Oktober 2018|title=Laksma TNI Muhammad Ali, S.E., M.M., Gubernur AAL Yang Baru|url=https://tni.mil.id/view-139288-laksma-tni-muhammad-ali-se-mm-gubernur-aal-yang-baru.html|website=Tentara Nasional Indonesia|language=id|archive-url=https://web.archive.org/web/20210422112456/https://tni.mil.id/view-139288-laksma-tni-muhammad-ali-se-mm-gubernur-aal-yang-baru.html|archive-date=22 April 2021|access-date=2021-04-22|url-status=live}}</ref>)
* Mayor Laut (P) [[Wirawan Ady Prasetya]] (2013-162013–16 Mei 2014<ref name=":0">{{Cite web|date=19 Mei 2014|title=Jabatan Komandan KRI Nanggala-402 Diserahterimakan|url=https://tni.mil.id/view-61587-jabatan-komandan-kri-nanggala-402-diserahterimakan.html|website=Tentara Nasional Indonesia|language=id|access-date=2021-04-21|archive-date=2021-04-22|archive-url=https://web.archive.org/web/20210422112501/https://tni.mil.id/view-61587-jabatan-komandan-kri-nanggala-402-diserahterimakan.html|dead-url=no}}</ref>)
* Mayor Laut (P) [[Harry Setyawan|Harry Setyawan, S.E.]] (16 Mei 2014<ref name=":0" />-8–8 Desember 2015<ref name=":1">{{Cite web|date=9 Desember 2015|title=Dua Kapal Selam TNI AL Berganti Komandan {{!}} WEBSITE TENTARA NASIONAL INDONESIA|url=https://tni.mil.id/view-88354-dua-kapal-selam-tni-al-berganti-komandan.html|website=Tentara Nasional Indonesia|language=id|access-date=2021-04-21|archive-date=2021-04-21|archive-url=https://web.archive.org/web/20210421123442/https://tni.mil.id/view-88354-dua-kapal-selam-tni-al-berganti-komandan.html|dead-url=no}}</ref>)
* [[Letnan Kolonel|Letkol Laut]] (P) Widya Poerwandanu (8 Desember 2015<ref name=":1" />-29–29 September 2016<ref name=":2">{{Cite web|date=29 September 2016|title=Komandan Kapal Selam Jajaran Koarmatim Berganti Tugas|url=https://www.tni.mil.id/view-103129-komandan-kapal-selam-jajaran-koarmatim-berganti-tugas.html|website=Tentara Nasional Indonesia|language=id|access-date=2021-04-21|archive-date=2021-04-22|archive-url=https://web.archive.org/web/20210422112511/https://www.tni.mil.id/view-103129-komandan-kapal-selam-jajaran-koarmatim-berganti-tugas.html|dead-url=no}}</ref>)
* Letkol Laut (P) Ahmad Noer Taufiq, S.T., M.Tr. Hanla. (29 September 2016<ref name=":2" />-2–2 Desember 2016<ref name=":3">{{Cite web|date=5 Desember 2016|title=Jabatan Komandan KRI Nanggala-402 Diserahterimakan|url=https://tni.mil.id/view-61587-jabatan-komandan-kri-nanggala-402-diserahterimakan.html|website=Tentara Nasional Indonesia|language=en|access-date=2021-04-21|archive-date=2021-04-22|archive-url=https://web.archive.org/web/20210422112501/https://tni.mil.id/view-61587-jabatan-komandan-kri-nanggala-402-diserahterimakan.html|dead-url=no}}</ref>)
* Letkol Laut (P) Yulius Azz Zaenal, S.H., M.Tr. Hanla. (2 Desember 2016<ref name=":3" />- 20–20 Februari 2019<ref name=":4">{{Cite web|date=20 Februari 2019|title=Sertijab Komandan KRI Nanggala-402 - ANTARA News Jawa Timur|url=https://jatim.antaranews.com/foto/278163/sertijab-komandan-kri-nanggala-402|website=Antara News|access-date=2021-04-21|archive-date=2021-04-21|archive-url=https://web.archive.org/web/20210421123443/https://jatim.antaranews.com/foto/278163/sertijab-komandan-kri-nanggala-402|dead-url=no}}</ref>)
* Letkol Laut (P) Ansori, S.H., M.H. (20 Februari 2019<ref name=":4" />-3–3 April 2020<ref name="Komando2020">{{Cite web|date=3 April 2020|title=Tongkat Komando Komandan Sekolah Awak Kapal Selam Beralih|url=https://tni.mil.id/view-174708-tongkat-komando-komandan-sekolah-awak-kapal-selam-beralih.html|url-status=live|access-date=2021-04-21|website=Tentara Nasional Indonesia|language=id|archive-date=2021-04-22|archive-url=https://web.archive.org/web/20210422112501/https://tni.mil.id/view-174708-tongkat-komando-komandan-sekolah-awak-kapal-selam-beralih.html|dead-url=no}}</ref>)
* Letkol Laut (P) Heri Oktavian (3 April 2020<ref name=":5" />{{snd}}21–21 April 2021)
== Struktur komando ==
| 