He attended military preparatory schools and graduated from the 23rd class of the Imperial Japanese Army Academy in December 1911, specializing in cavalry operations.

In 1919, he graduated from the 31st class of the Army War College and was promoted to the rank of captain in the cavalry.

In December 1940, he was promoted to lieutenant general and commander of the IJA 5th Air Group in Taiwan, where he was stationed at the start of the Pacific War.

However, at the Battle of Guam he ordered an all-out attack at midnight, 25 July 1944, but was soon overwhelmed by superior American numbers and firepower, losing more than 80% of his men.

Obata committed seppuku on 11 August 1944 in Yigo, Guam, ending Japanese attempts to hold the island.