Sebelum berlakunya Perang Dunia II di Pasifik, pulau Borneo dibahagikan kepada lima wilayah. Empat wilayah di utara dan di bawah kawalan British - Sarawak, Brunei, Labuan (pulau), dan British Borneo Utara; manakala sisanya dan sebahagian besar pulau di selatan di bawah bidang kuasa Hindia Timur Belanda.
Pada 16 Disember 1941, pasukan Jepun mendarat di Miri, sebahagian wilayah utara British, dari Teluk Cam Ranh di Indochina Perancis. Selepas pendaratan, angkatan tentera Jepun mengambil masa kurang daripada sebulan untuk mengatasi wilayah-wilayah dan kemudian menamakan semula bahagian utara sebagai Borneo Utara (北 ボ ル ネ オ Kita Boruneo), Labuan sebagai Maida Island (前 田島 Maeda-shima) dan wilayah Belanda yang berdekatan sebagai Borneo Selatan (南 ボ ル ネ オ Minami Boruneo) dengan nama-nama Jepun.[4][5][6] Buat pertama kali dalam sejarah moden, kedua-dua wilayah, yang telah lama dipisahkan di bawah peraturan penjajah Barat, telah bersatu di bawah pemerintahan penjajah Jepun dengan seluruh penduduknya menjadi mata pelajaran maharaja Jepun.[7]
Wilayah-wilayah diperintah selama tiga tahun, di mana pihak berkuasa Jepun secara aktif menggalakkan pembiasaan budaya Jepun (penjepunan) dalam kalangan penduduk tempatan pulau itu dengan menghendaki mereka memasuki kelas bahasa Jepun. Jepun membahagi wilayah utara ke lima wilayah pemerintahan (洲shu) dan membina lapangan terbang. Beberapa kem perang dikendalikan di seluruh pulau di mana kebanyakan pegawai penjajah Barat ditahan bersama dengan anggota gerakan bawah tanah yang menentang pemerintahan yang keras semasa pendudukan Jepun. Sementara itu, kedudukan pemimpin Melayu tempatan dikekalkan dengan pengawasan Jepun dan kebanyakan bidang tenaga kerja dipenuhi oleh orang-orang latar belakang Asia yang berbeza.
Menjelang akhir tahun 1945, komando Australia mula dikerahkan ke pulau itu oleh kapal selam AS di mana Unit Khas Bersekutu Z menjalankan operasi perisikan dan melatih seribu orang orang asli untuk melawan Jepun dalam peperangan gerila di bawah Kempen Borneo sambil bersiap sedia untuk bersekutu utama misi kemerdekaan. Berikutan pertempuran Borneo Utara dan Labuan dari 10 Jun 1945 dengan gabungan pasukan Australia dan Amerika, pulau Borneo dibebaskan dengan Pentadbiran Tentera Jepun digantikan dengan Pentadbiran Tentera British pada 12 September 1945.
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