Indian tribal governments operate independently of the federal United States government, with some caveats. There are some policies that govern how and when the United States may intercede over Indian tribal sovereignty, and the rights that Indian tribal governments have with their land. This operates much like diplomatic and trade agreements.
As recognition for the Native American population existing in the United States prior to the United States, the US allows Indian tribal governments to operate with certain freedoms and liberties, such as being able to manage their own population on their land. However, for pragmatic reasons, Indian tribal citizens still need to be able to take advantage of many resources from the United States, and vice versa. Consequently, there’s an extremely tight set of regulations regarding how Indian tribal governments relate to the United States government.
As an example, Indian tribal businesses are not required to have an EIN, because they aren’t required to file federal taxes or pay federal taxes. However, it’s possible for an Indian tribe to have distributions and income that are taxable to recipients.