Unlike Hsinchu's experimental primary and middle schools, which are under the jurisdiction of the Administrative Yuan's National Science Council, STSIP's public primary and middle schools are covered by the Tainan County Bureau of Education, and are ranked at the same level as all public primaries, enjoying no special privileges.
和竹科的實驗中小學隸屬於行政院國科會不同的是，南科國中和國小隸屬於台南縣教育局，定位上就和一般的國民小學一樣，並沒有享受什麼「特權」。