As part of the United State's policy of assimilation in order to take care of the "Indian problem," Indian religious beliefs were discouraged and often banned on reservations or as part of government of missionary run day schools and boarding schools (the idea being to "kill the Indian and save the man"—since it was the Indian's "savage" and "primitive" culture holding him back, extinguishing it and replacing it with the Western Judeo-Christian "white" culture would allow him to become part of "civilization").
With the grant of citizenship to all Indians in the United States ( Indian Citizenship Act of 1924), this should not have been a problem, as they should have been accorded all the rights inherent under US citizenship—which, of course, includes First Amendment rights ("Congress shall pass no law respecting an establishment of religion, or prohibiting the free exercise thereof"). Unfortunately this has not always been the case.
Besides examples from schools, the most clear problems have been in dealing with prisoners. While most prisoners have relatively fair allowances to the practice and exercise of their religious rights, Indians generally have not. As in schools, a small part of the blame comes from ignorance and unfamiliarity with the various religious practices—on the other hand (as with the schools and American society, in general), there is almost always an implicit, and sometimes all too common, explicit Judeo-Christian (more at Christian) chauvinism that exists, well-known to others of minority religious beliefs (or lack thereof).
Prisoners had really no legal protection from what could be deemed (rather arbitrarily) but officials as a "security risk." Among these: " sweatlodges, long hair worn in a traditional fashion, headbands, medicine bags, possession of sage, cedar, and tobacco and other practices have been banned as 'security risks' by one prison or another" (http://theofficenet.com)—things that have been shown to help the rehabilitation of the incarcerated in many cases (this should be no surprise when there are so many examples of inmates turning their lives around following their "finding" of God/Jesus/Allah while in prison).
Other difficulties facing Indians were not being allowed near sacred land to perform ceremonies, use of controlled substances (more below), and use of objects, such as eagle feathers, which come from endangered species.
In 1978, Congress made an attempt to "restore" the religious rights of Indians (which were supposed to already exist) through the American Indian Religious Freedom Act (sometimes referred to as AIRFA). The original had additional material (below) that states, among other things, that "the lack of a clear, comprehensive, and consistent Federal policy has often resulted in the abridgment of religious freedom for traditional American Indians." The current text of the act as it appears in the United States Code (as of 5 January 1999) follows—the substance and wording of the act is essentially the same, except for the prior material and a transition between the two:
Whereas the freedom of religion for all people is an inherent right, fundamental to the democratic structure of the United States and is guaranteed by the First Amendment of the United States Constitution;
Whereas the United States has traditionally rejected the concept of a government denying individuals the right to practice their religion and, as a result, has benefited from a rich variety of religious heritages in this country;
Whereas the religious practices of the American Indian (as well as Native Alaskan and Hawaiian) are an integral part of their cultures, tradition and heritage, such practices forming the basis of Indian identity and value systems;
Whereas the traditional American Indian religions, as an integral part of Indian life, are indispensable and irreplaceable;
Whereas the lack of a clear, comprehensive, and consistent Federal policy has often resulted in the abridgment of religious freedom for traditional American Indians;
Whereas such religious infringements result from the lack of knowledge or the insensitive and inflexible enforcement of Federal policies and regulations premised on a variety of laws:
Whereas such laws were designed for such worthwhile purposes as conservation and preservation of natural species and resources but were never intended to relate to Indian religious practices and, therefore, were passed without consideration of their effect on traditional American Indian religions;
Whereas such laws and policies often deny American Indians access to sacred sites required in their religions, including cemeteries;
Whereas such laws at times prohibit the use and possession of sacred objects necessary to the exercise of religious rites and ceremonies;
Whereas traditional American Indian ceremonies have been intruded upon, interfered with, and in a few instances banned: Now, therefore, be it...
US Code : Title 42, Section 1996
Sec. 1996. Protection and preservation of traditional religions of
Native Americans
On and after August 11, 1978, it shall be the policy of the United States to protect and preserve for American Indians their inherent right of freedom to believe, express, and exercise the traditional religions of the American Indian, Eskimo, Aleut, and Native Hawaiians, including but not limited to access to sites, use and possession of sacred objects, and the freedom to worship through ceremonials and traditional rites.
This was a nice step, but the act had no significant legal force, as was found in 1988 (Lyng v. Northwest Indian Cemetery Protective Association) when the Supreme Court ruled that it was only a "policy statement" and is "judicially unenforceable. If a federal agency does not abide by the policy, AIRFA does not provide any legal recourse for tribes, groups, or individuals" (www.nativenashville.com). While admitting an obligation to "protect and preserve," no provisions were made for doing so and no way to enforce it when violations occur.
In 1993, the Religious Freedom Restoration Act (RFRA) was passed which did provide protection to Indians—and others, not being specifically aimed at Indians. (Though it can be seen, in part, as a response to the Employment Division v. Smith Supreme Court Case discussed below.) The RFRA introduced a "compelling interest" test which stated that the government was not allowed to place restrictions on religious practices unless it was able to show compelling interest to do so. This meant (in the examples above) that officials could no longer merely assert something to be a "security risk," but had to show that it was. It also gave the right to seek judicial proceedings in the case the person felt those religious rights were violated.
Unfortunately, the 1993 act was ruled unconstitutional in 1997 (City of Boerne Texas v. Flores) as it was felt it gave religious groups more protection than individuals or non-religious groups or individuals, violating the establishment clause. It was seen as permitting those groups/individuals more protection over non-religious or "irreligious" groups/individuals. Not surprisingly, among those opposed to it were people in the corrections "industry" that were concerned that prisoners would only use the right to mask illegal behavior. (Another group being atheists. As quoted at www.religioustolerance.org: "Justice John Paul Stevens stated that the Act violated the principle of separation of church and state, by preferring 'religion over irreligion.' This gave to religious groups special privileges which 'no atheist' could hope to attain," italics in not mine.)
There was an amendment to the AIRFA in 1994. It stemmed from a 1990 Supreme Court case (Employment Division v. Smith) involving two counselors who had been fired from their jobs for using peyote (not at work)—working in a chemical dependence program, they had promised not to take any addictive substances. Since they were Indians and belonged to the Native American Church, the taking of the peyote was "sacramental" in nature. Part of the reason the Court ruled against them was that the law re peyote was not directed at the religious practice (or at Indians) and therefore was not in violation of the constitution (it was also seen as a state's rights case, in part). The subsequent amendment to the act was meant to rectify that by allowing its use as part of Indian religious ceremonies, while remaining a controlled substance.
An interesting part of the amendment is that it states that it should not be "construed as requiring prison authorities to permit, nor shall it be construed to prohibit prison authorities from permitting, access to peyote by Indians while incarcerated within Federal or State prison facilities."
It should be noted that despite the ruled unconstitutionality of the RFRA, many states have passed similar legislation (part of the Supreme Court's decision was due to its conclusion that the federal act took away the states' rights to enforce their laws).
(Sources: http://theofficenet.com/~redorman/lfoster2.htm, www.nativenashville.com/History/preservation_airfa.htm, www.religioustolerance.org, www.sbs.uab.edu/history/varticles/Nacsac.htm, the preface to the act was at www.cortland.edu/www/philosophy/airfa.html, and the act can be found at www4.law.cornell.edu)