One suspect was dragged out of the courtroom by military guards and one defense lawyer was rushed to the Gitmo hospital after suffering an unspecified illness, The Miami Herald reported.
The most well-known of the defendants, alleged 9/11 mastermind Khalid Sheik Mohammad, is charged with four other men with conspiring to carry out the 2001 attacks in New York City and Washington, D.C.
The hearing, which was to last a week, was meant to address ongoing computer problems defense lawyers said have led to a violation of attorney-client privilege. The lawyers said faulty U.S. Department of Defense computer systems have led to the inadvertent deleting of emails and other documents in the case.
The hearing was to determine how to fix the problems and whether to proceed with the case while technical improvements are instituted.
But that rather unemotional topic quickly turned heated when Mohammad began reading aloud in court from what appeared to be a prepared statement in Arabic protesting his lack of access to legal counsel.
Co-defendant Ramzi bin al-Shibh then jumped to his feet and began yelling about his right to be heard in court, the Herald said.
"I have a right to talk!" he shouted.
"No you don't!" the Army judge, Col. James Pohl, shouted back before ordering military personnel to remove al-Shibh from the courtroom.
The hearing met an abrupt end shortly thereafter when Pohl excused defense lawyer Cheryl Bormann, a death penalty expert, for an illness.
"Don't take this the wrong way but, you sound horrible," Pohl told Bormann.
Because the five men are being tried together, Bormann's absence forced a recess for the day. It was unclear when, or if, the technical hearing would resume.