Seven of the accused appeared in straitjackets under tight security in the court in the eastern district of Sabah, the Philippine Daily Inquirer reported Thursday.
None of the accused, who are between the ages of 17 and 66, were represented by counsel and none of them entered a plea.
The judge ordered the attorney general to determine whether the Bar Council of Malaysia, the Philippine government or the accused themselves would find lawyers for the defendants.
The Filipinos are among 107 suspected Sulu gunmen or local supporters of Sultan Jamalul Kiram III of Sulu arrested by Malaysian forces after Kiram's "royal army" occupied a village in Lahad Datu last month.
Some 62 Sulu rebels and 10 Malaysian soldiers and police officers have been killed since March 5, when the Malaysian government launched an assault on the group's members in the districts of Lahad Datu, Tawau, Kunak, Sandakan and Semporna.