In his ruling, Marine Col. Ralph Kohlmann said the military commission found that the interests of justice in the complex legal case would be best served by completing the arraignments on June 5.
"It is precisely because of the anticipated complexity of this case that it is important that the process get under way," Kohlmann said in the ruling, which was obtained by The Associated Press.
Military lawyers had sought to postpone the first pretrial hearings for men charged with the 2001 attacks that killed almost 3,000 people in New York, Washington and Pennsylvania, saying the government has made it impossible to defend them.
The highly anticipated arraignments are scheduled for June 5 at this remote U.S. Navy base in Guantanamo Bay, Cuba. The U.S. is seeking the death penalty for all five defendants, including confessed mastermind Khalid Sheikh Mohammed.
Defense lawyer and Army Maj. Jon Jackson, who represents Saudi detainee Mustafa al-Hawsawi, said he was disappointed by Kohlmann's ruling.
"Mr. Hawsawi has been held for more than four years without a hearing or access to a lawyer. Now he is being rushed into the courtroom after only two meetings with me, his lead counsel," Jackson said Thursday.
Jackson also said the facilities for defense preparation at the isolated tropical base are "completely inadequate for this type of proceeding."
In his ruling, Kohlmann said concerns expressed by the defense regarding their working spaces in Guantanamo and Washington was not a matter that justified a delay.
"It appears that progress is being made with regard to dealing with the logistic challenges associated with this case. It is likely that the lawyers' tasks in this case are going to be difficult in several regards," Kohlmann said.
Military defense lawyer Navy. Lt. Cmdr. Brian Mizer said he had expected the judge to deny the defense request because he believes the tribunal system to be profoundly flawed.
"It should not be surprising that the same system that does not afford an accused the right to remain silent or to confront his accusers will also not allow him to meet his attorneys before the United States begins its prosecutorial effort to execute him," Mizer said. "At this point, I would not be surprised if the prosecution attempted to seat 12 monkeys as jurors."
Mizer was appointed to represent Ali Abd al-Aziz Ali, known as Ammar al-Baluchi, a nephew and alleged lieutenant of Khalid Sheikh Mohammed.
The other two suspects are Ramzi Binalshibh, said to have been the main intermediary between the hijackers and leaders of al Qaeda, and Waleed bin Attash, a detainee known as Khallad, who investigators say selected and trained some of the 19 hijackers.
The Pentagon dropped charges earlier this month against a Saudi at Guantanamo, Mohammed al-Qahtani, who was supposed to have been the "20th hijacker" in the Sept. 11 attacks. Authorities have alleged that al-Qahtani barely missed out on taking part in the attacks because a U.S. immigration agent denied him entry when he arrived at the airport in Orlando, Florida.
Prosecutors have been working for years to assemble the case against suspects in the attacks that prompted the administration of U.S. President George W. Bush to launch its global war on terror.
The arraignments will likely precede a Supreme Court ruling on the legitimacy of the first U.S. war-crimes trials since World War II. The court is expected to rule before June 30 whether the 270 men held at Guantanamo have access to regular U.S. courts, which could undermine the military trials.
The Court declared a previous military tribunal system unconstitutional in 2006.