The problems incidental to placing the students permanently in preparatory schools and colleges were great, as a review of Superintendent Sutherlands’s early reports will reveal. His fears regarding the schools in states having large negro populations were justified. “....Not the school, but the sentiment is at fault,” he reported. And while for reasons of climate,  system of education, and other cogent ones, this section should have been the one, logically to receive the students, in their major part, in order to avoid all possibility of unpleasantness or mistreatment, no students are to be placed at any point where they will be thus exposed.”[1] Nevertheless, five students were enrolled in the law department of the University of Tennessee at Knoxville—”the Southernmost school in which I feel safe in locating my dark-complexioned charges…”[2] There was evidence of discrimination against Filipinos elsewhere, as in Indiana, where a bill was introduced in the state legislature to prohibit marriage between Filipinos and Americans.[3] “It was found,” Sutherland reported, “That while the proposed bill seemed to be aimed especially at the Students attending the University of Indiana at Bloomington, the students themselves had given no reasonable cause to presume that such a measure was for.”[4] Sutherland explained the United States Government’s attitude toward the classification of Filipinos as negroes[5] to several state senators, including the one who had introduced the measure, and was informed that the bill would not be pressed to passage.[6]
            Further difficulties were encountered when Catholic organizations and the Catholic press in general became critical of Sutherland’s apparently accidental policy of placing the pensionados in non-Catholic institutions. The Catholic argument was to the effect that sufficient care had not been taken by the Philippine government in ensuring to the students the same religious influence that surrounded them at home and that should be continued to them there. [7] Sutherland explained to Colonel Edwards that none of the schools attended by the students had been selected either for its religious influences or on account of the lack of them. “I have deemed it of the utmost importance,” he wrote to avoid any just criticism by either Catholics or non-Catholics and have therefore entirely disregarded all of my actions in this connection to the matter of denomination in the school selected.” In the absence of any stated preference of the student or his parents, therefore, the criteria upon which his selections and recommendation had been based were 1. The suitability of the school to the needs of the student in the matter of courses offered; 2. The cost of living of the locality; and 3. The standard of refinement and the morality of the community. It could not be said that the state institutions were denominational, and the private institutions to which the Filipinos had been sent weren't denominational in the sense that attendance at religious services was required. Nor was “any official notice taken by the authorities of the schools of the religion of the pupils nor any attempt made by them to influence in any way, much less to coerce, the students in their religious practices.”[8]
            Similar sentiments were expressed in Professor Sutherland’s “Open Letter” of October 1, 1904 to Joseph A. Weber, Secretary of the Federation of Catholic Societies at Philadelphia. Replying to the charge that Secretary Taft, Colonel Edwards and those having these matters in charge, have selected denominational, Protestant Schools for the education of the Filipino government students, to the exclusion of Catholic schools, with the deliberate intention of proselytizing the said students, or as one paper states it, for their “protestantization,” Sutherland declared that he could not but believe that such a view must arise from the “inexcusable ignorance.” “Is this a Catholic School or a Protestant School? Has never been asked in consideration of the merits of a school for the Filipino Students…” “I will say,” he wrote, “that not a single one of the Filipino students during all the innumerable consultations that we have had on the subject of the school that they were to attend has ever asked me to be placed in a school because it was Catholic. We have never in a single case discussed the religion or denomination of a school that they were to attend , for its selection or rejection.”[9]
            On October 10, 1904, Colonel Edwards cabled Governor Wright, calling attention to the religious issue. Notre Dame, he said, has just waived tuition fees: it would relieve embarrassment if an announcement could be made that some of the twenty-eight students then en route from Manila could be assigned there. [10] Wright responded by cable on October 11 that he could see no objection to assigning Catholic students to Catholic schools. [11] On the same date, President Roosevelt sent the following telegram to Secretary of War Taft:

There are certain subjects which, as I am informed are not taught in Catholic colleges, or at least are not taught at all as they are taught in various State and non-sectarian colleges. These subjects are not engineering, architecture, and kindred matters of a technical nature. The Filipino students who wish to take courses of this kind will of course be allotted to colleges like the institutes of technology, polytechnic institutes, state agricultural colleges, and so forth. Academic, commercial, and law courses can be followed at the Catholic colleges, and Filipino students who are Catholics desiring to follow these courses, unless they express a wish to the contrary, must be given the chance to go to these Catholic colleges, and the offer to the Catholic colleges must be made in writing in terms that are impossible of misunderstanding.[12]

            Finally, October 17, Secretary Taft ruled that in a “system of public instruction in which the pupils are only in the school for a few hours during the day, and are still subject completely to the moral and religious teaching of their parents, and their home church, the government may properly decline the responsibility for the religious education of the pupils, but when the government takes pupils from their homes into a new and strange country, it can not properly rid itself of responsibility for the continuance of the same moral and religious surroundings that its wards had at home.” Sutherland was therefore directed to secure statements from the parents or guardians of pupils under twenty-one, or from the students who are twenty-one or over, as to their religious faith and as to whether attendance at a denominational school was desired. Every effort, the Secretary said, should be mated to comply with the wishes of the adult student or of the parent or guardian. “...Mr. Sutherland should consult the ministers of the pupils’ religion resident in the neighborhood where the pupil will pursue his studies and invoke the aid of such ministers, not only in securing a proper boarding place but also in using their moral and religious influence upon the pupil to keep him on the path he should go.”[13]