Soja refers to a shrine that has collected gods of local shrines and enshrined them together. Some shrines were those put together in a ryoseikoku (province), and others were those in a private estate or village. Other were those in a gun (district) or a go (region).
Soja in province
In ancient Japan, the first task of kokushi (provincial governors) was to visit and worship at all the shrines within the province. During the Heian period, establishing a soja near the kokufu (provincial office) and worshiping at it became wide spread to save the tour of every shrine. This is why the soja was generally located near the kokufu. A large number of soja once disappeared in the medieval period and some revived later. Others have not revived yet or no body knows which used to be soja.