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In spite of the difficulties of the conquest, and before it was even complete, from the 1860s the admirals began to put an administrative and political infrastructure into place. They held almost absolute power in Cochinchina, in accordance with the French colonial model of direct administration that had been tested in the “old colonies” (the French West Indies, La Réunion), which made easier by the exile of the mandarins. From 1861 the colony was run by a governor based in Saïgon. He was assisted by a Privy Council, which was a consultative assembly made up of senior civil and military officials. After 1864, the Department of the Interior took control of the entire administrative apparatus. The twenty-one provinces were under the supervision of an official, initially a naval officer, then later inspectors of indigenous affairs. Cholon and Saïgon acquired the status of municipalities. The so-called "government of Admirals" put in place the institutions for raising taxes in the colony and promoting economic development, as well as for the overall enhancement of the territory. 1862 saw the creation of the "Opium Farm" (which was taken into state ownership in 1881), the Department of Registration and Property (Land Registry department) and the Telegraph Service (1861-1862). The Department of Public Works was set up in 1863 followed by the Bank of Indochina in 1873. The machinery of repression was also put into place, with the establishment of the central prison in 1861 and the penal colony of Poulo Condore in 1862.

After coming to power in 1879, the Republicans established a more rational civil administration that separated powers which until then had been concentrated in the hands of the admirals, as well as applying the principle of assimilation. The naval officers, who had been heavily criticized by the settlers, were removed and Le Myre de Vilers became the first civilian Governor of Cochinchina. The Colonial Council, a deliberative assembly that was created in 1880 consisted of both French and Vietnamese elected worthies. From 1881, Cochinchina elected a deputy to the French national parliament, enabling it to play a political role in mainland France.