It is larger than an actual settlement, being in actuality a subdivision of a rural district, districts are subdivided into towns and villages, with no overlap, and no uncovered area.
Generally, a village or town can be promoted to a city when its population increases above fifty thousand, and a city can (but need not) be demoted to a town or village when its population decreases below fifty thousand.
A city (市 shi) is a local public body in Japan, part of a prefecture (ken or other equivalents).
A municipality or "general-purpose district" (compare with: "special-purpose district") is an administrative local area generally composed of a clearly defined territory and commonly referring to a city, town, or village government.