| Escort Fleet (Yokosuka) |
DDG168 Tachikaze (Yokosuka) (*) | ||
| 1st Escort Flottila (Yokosuka) |
DDH143 Shirane (Yokosuka) (*) | ||
| 1st Escort Squadron (Yokosuka) | DD101 Murasame | ||
| DD102 Harusame | |||
| 5th Escort Squadron (Yokosuka) | DD107 Ikazuchi (as of March 14, 2001) |
||
| DD154 Amagiri | |||
| DD158 Umigiri | |||
| 61st Escort Squadron (Yokosuka) | DDG171 Hatakaze | ||
| DDG174 Kirishima | 2nd Escort Flottila (Sasebo) |
DDH144 Kurama (Sasebo) (*) | |
| 2nd Escort Squadron (Sasebo) | DD151 Asagiri | ||
| DD152 Yamagiri | |||
| DD157 Sawagiri | |||
| 6th Escort Squadron (Sasebo) | DD103 Yuudachi | ||
| DD104 Kirisame | |||
| 62nd Escort Squadron (Sasebo) | DDG170 Sawakaze | ||
| DDG173 Kongo | |||
| 3rd Escort Flottila (Maizuru) |
DD141 Haruna (Maizuru) (*) | ||
| 3rd Escort Squadron (Maizuru) | DD124 Mineyuki | ||
| DD126 Hamayuki | |||
| 7th Escort Squadron (Ohminato) | DD153 Yuugiri (as of March 14,2001) |
||
| DD155 Hamagiri | |||
| DD156 Setogiri | |||
| 63rd Escort Squadron (Maizuru) | DDG172 Shimakaze | ||
| DDG175 Myoko | |||
| 4th Escort Flottila (Kure) |
DDH142 Hiei (Kure) (*) | ||
| 4th Escort Squadron (Kure) | DD105 Inazuma | ||
| DD106 Samidare | |||
| 8th Escort Squadron (Kure) | DD130 Matsuyuki | ||
| DD131 Setoyuki | |||
| 64th Escort Squadron (Sasebo) | DDG169 Asakaze | ||
| DDG176 Chokai | |||
| ATS4202 Kurobe (Kure) | |||
| ATS4203 Tenryu (Kure) | |||
| AOE421 Sagami (Sasebo) | |||
| AOE422 Towada (Kure) | |||
| AOE423 Tokiwa (Yokosuka) | |||
| AOE424 Hamana (Sasebo) | |||
| Submarine Fleet (Yokosuka) |
1st Submarine Flottila (Kure) | ASR403 Chihaya (Kure) (*) | |
| ASU7020 Hayase (Kure) | |||
| 1st Submarine Squadron (Kure) | SS577 Nadashio | ||
| SS591 Michishio | |||
| SS593 Makishio (as of March 29, 2001) |
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| 3rd Submarine Squadron (Kure) | SS585 Hayashio | ||
| SS586 Arashio | |||
| SS588 Fuyushio | |||
| 5th Submarine Squadron (Kure) | SS579 Akishio | ||
| SS583 Harushio | |||
| SS584 Natsushio | |||
| 2nd Submarine Flottila (Yokosuka) | ASR405 Chiyoda (Yokosuka) (*) | ||
| 2nd Submarine Squadron (Yokosuka) | SS590 Oyashio | ||
| SS592 Uzushio | |||
| 4th Submarine Squadron (Yokosuka) | SS580 Takeshio | ||
| SS581 Yukishio | |||
| SS582 Sachishio | |||
| 6th Submarine Squadron (Yokosuka) | SS578 Hamashio | ||
| SS587 Wakashio | |||
| 1st Submarine Training Squadron (Kure) | TSS3601 Asashio | ||
| TSS3603 Okishio (ex-SS576, as of March 14, 2001) |
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| Mine Sweeping Flottila | MST463 Uraga (Yokosuka) (*) | ||
| MST464 Bungo (Kure) | |||
| 1st Mine Sweeping Squadron (Kure) | MSC678 Tobishima | ||
| MSC679 Yugeshima | |||
| MSC680 Nagashima | |||
| 2nd Mine Sweeping Squadron (Sasebo) | MSC665 Himeshima | ||
| MSC666 Ogishima | |||
| MSC684 Naoshima (as of March 16, 2001) |
|||
| 3rd Mine Sweeping Squadron (Yokosuka) | MSC681 Sugashima | ||
| MSC682 Notojima | |||
| MSC683 Tsunoshima | |||
| 51st Mine Sweeping Squadron (Yokosuka) | MSO301 Yaeyama | ||
| MSO302 Tsushima | |||
| MSC303 Hachijo | 101st Mine Sweeping Squadron (Kure) | MCL722 Niijima (ex-MSC655) | |
| MCL723 Yakushima (ex-MSC656) | |||
| 1st Transport Squadron (Yokosuka) | LST4152 Ojika | ||
| LST4153 Satsuma | |||
| LST4001 Osumi (Kure) | |||
| 21st Escort Squadron | DD122 Hatsuyuki |
| DD123 Shirayuki | |
| DD125 Sawayuki (as of March 14, 2001) |
|
| 41st Mine Sweeping Squadron | MSC668 Yurishima |
| MSC670 Awashima | |
| MSC671 Sakushima | |
| LCU2002 | |
| AGB5002 Shirase |
| 22nd Escort Squadron | DD129 Yamayuki (as of May 18, 2001) |
| DDE225 Noshiro | |
| 42st Mine Sweeping Squadron (Hanshin) |
MSC674 Tsukishima |
| MSC676 Kumejima | |
| LSU4171 Yura |
| 23rd Escort Squadron | DD127 Isoyuki |
| DD128 Haruyuki | |
| DD132 Asayuki | |
| 26th Escort Squadron | DE231 Oyodo |
| DE232 Sendai | |
| DE234 Tone | |
| 43rd Mine Sweeping Squadron (Shimonoseki) |
MSC673 Ieshima |
| MSC675 Maejima | |
| MSC677 Makishima | |
| 46th Mine Sweeping Squadron (Okinawa) |
MSC667 Moroshima |
| MSC669 Hikoshima | |
| LCU2001 |
| 24th Escort Squadron | DD164 Takatsuki |
| DD165 Kikuszuki | |
| 31st Escort Squadron | DE229 Abukuma |
| DE230 Jintsu | |
| 44th Mine Sweeping Squadron | MSC661 Takashima |
| MSC662 Nuwajima | |
| MSC663 Etajima | |
| LSU4172 Noto |
| 25th Escort Squadron | DD121 Yugumo |
| DE233 Chikuma | |
| 27th Escort Squadron | DE226 Ishikari |
| DE227 Yubari | |
| DE228 Yubetsu | |
| 44th Mine Sweeping Squadron (Hakodate) |
MSC660 Hahajima |
| MSC664 Kamishima | |
| MSC672 Uwajima | |
| 1st Missle Boat Squadron (Amarushi) |
PG821 |
| PG822 | |
| PG823 | |
| LST4103 Nemuro |
| TV3508 Kashima (Kure)(*) | |
| 1st Training Squadron (Kure) | TV3512 Aokumo (ex-DD119) |
| TV3513 Shimayuki(ex-DD133) | |
| TV3514 Akigumo(ex-DD120) |
| as of December 1, 2000 | MSC659 Torishima |
| as of March 30, 2001 | TSS3602 Setoshio (ex-SS575/ATSS8008) |
| as of May 15, 2001 | DDE223 Yoshino |
| as of May 18, 2001 | DDE224 Kumano |