Japan did not conquer Vietnam, it had already been conquered by the French. For most of the war Japan left the existing French colonial government in place and negotiated the rights to station troops there and move them through the country.
Initially, Japan was only interested in Northern Indochina to cut off supplies to China. To this end they signed an accord with Vichy France in Sept 1940 to be able to station and move a limited number of troops through French Indochina (modern Laos, Cambodia, and Vietnam). The Japanese immediately violated this but eventually things settled down. Japan did not advance further south for fear of antagonizing the US and Britain.
In October 1940 Thailand took the opportunity of France's weakness to win back territory lost in the Franco-Siamese War of 1893. After defeats for the French, the Japanese stepped in to mediate a cease-fire in January 1941. France ceded disputed border provinces to Thailand.
Realizing they could no longer defend their overseas territories, and not being at war with Japan, in July 1941 Vichy France signed the "Protocol Concerning Joint Defense and Joint Military Cooperation". This secured Indochina for the Vichy French and gave the Japanese airfields and bases close to attack South East Asia.
This state of affairs of mostly peaceful cooperation between the French colonial government and Japanese military continued until almost the end of the war. In March 1945, with France restored and the war turning against them, the Japanese launched a coup d'état in Indochina. They redeployed their troops to surround the French garrisons and suddenly ordered them to disarm. Fighting was brief, and in a single day the Japanese dismantled French rule in Indochina.
The Japanese split Indochina into three puppet states under sympathetic rulers: the Empire of Vietnam, the Kingdom of Kampuchea (Cambodia), and the Kingdom of Laos and made them all part of the Greater East Asia Co-Prosperity Sphere.
By handing Vietnam independence from French colonial rule, and eventually allowing reunification of north and south Vietnam, Japan avoided a fight with the native populations. Once the Empire of Japan fell, the short lived Empire of Vietnam did as well and the Viet-Minh took over in the August Revolution.