We don't often see gods depicted as dwarves. Rather, most of them are physically depicted as strong and tall.
I have found the Egyptian God Bes, but is there another dwarf god known to him?
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In The Lives of Dwarfs: Their Journey from Public Curiosity toward Social Liberation, Betty Adelson identifies Sukuna-biko, an ally of Okuninushi in Shinto mythology, as an example of a dwarf god:
In a Japanese tale, the Great-Land-Master, an excellent and just ruler, is standing on the shore when a dwarf god named Suku-na-biko, "The Small Renown Man," comes in from the sea on a raft, wearing a mantle of feathers and dressed in moth's wings. The dwarf tells the Great-Land-Master that he is the son of the Divine-Producing goddess and expert at the healing arts. A close friendship develops and the two collaborate at cultivating medicinal plants and curing disease. Despite being unable to walk on his tiny legs, Suku-na-biko knows everyone and goes everywhere. Ultimately, he climbs on a millet stalk, which bounces back and sends him to Tokyo, the Land of Eternity. Even today his name is often invoked for medical assistance, and he is called upon to lead people to curative springs.