These are from two different dictionaries and they are not even contemporary. One is 10 years older than the other. (If AI search is to be believed.) Even so I don't think these two definitions are incompatible. They both say it was the lowest officer rank.
Lieutenant [尉官]: The rank below officer. The lowest rank among the three main divisions of officers in the Army, Navy, and Air Force. (Shin Meikai Japanese Dictionary, 7th Edition, p. 63)
Lieutenant [尉官]: Corresponding to the ranks of Captain, Lieutenant, and Second Lieutenant in the former Army, Navy, and Air Force, below General Officers and Senior Officers. (Meikyo Japanese Dictionary, 3rd Edition, p. 79)