More than 20 people detained in Uganda in connection with the massacre at the school on Friday are being held on charges of working together with the rebel group accused of carrying out the killings.
The director and headteacher are two of those detained but they have made no comments.
According to officials, there may have been a dispute over who owned the school where 42 people died.
The army claims that militants connected to the Islamic State were responsible for the attack, but other motives are being looked into.
They are members of the Allied Democratic Forces (ADF), an organization founded in the 1990s that fought President Yoweri Museveni on the grounds that Muslims were being persecuted. The neighboring Democratic Republic of the Congo is now where it is based in large part.
With regard to whether locals and those in charge of the kids were involved, the arrests raise challenging questions.
However, the situation is not very clear.
In the small town of Mpondwe, close to the border with the DR Congo, the Lhubiriha Secondary School was attacked late on Friday, resulting in the deaths of 37 students.
The victims, many of whom were dorm residents, were burned alive or killed by knives, and some may have also been shot.
In the immediate aftermath of the assault, army commander Maj Gen Dick Olum claimed that the ADF had used the violence to divert his soldiers' attention away from their pursuit of the insurgents inside the DR Congo.
The BBC was informed by a neighbor that she overheard one of the attackers yelling "Allahu Akbar," which is Arabic for "God is greatest," and "we have succeeded in destabilizing Museveni's country.".
It is believed by military intelligence that five ADF militants took part in the assault.
Despite having previously attacked in Uganda, the ADF, which is now believed to be affiliated with the IS group, has not yet claimed responsibility for the attack.
President Museveni has mentioned "wrangles" over the school in addition to blaming "the terrorists of the ADF" for what occurred. However, he has not gone into further detail.
First Lady Janet Museveni, who also serves as education minister, claimed there had been a "conflict" between the non-governmental organization (NGO) that built it and "groups in [the district of] Kasese who wanted to take it over.".
Despite the fact that auditors from the NGO had visited the school the day before the attack, she emphasized that a proper investigation was ongoing on Saturday.
According to Brig Gen Felix Kulayigye, spokesman for the Ugandan army, two individuals accused of leading the attackers "to avoid detection" in Mpondwe have also been detained along with school officials.
