In May, parliament abolished state security courts but that order does not come into force for about another month. The reform was approved as part of Turkey's bid to join the European Union.
In a written ruling, the court said that due to the changes it no longer had the authority to hear the case. All 69 defendants, however, must still appear before the court this week on procedural grounds. The court, however, will not hear their testimony.
Turkish authorities are expected to set up new tribunals in the coming months that will deal with "terrorism" and other cases.
The twin attacks on 15 and 20 November, blamed on local hardliners with alleged links to the al-Qaida network, saw human bombers drive trucks laden with powerful bombs to two synagogues, the British consulate and a branch of the British-based HSBC bank, triggering massive explosions with devastating results.
The heaviest charge - "attempting to change the constitutional order by force" - has been brought against five defendants described as the leaders of the al-Qaida cell in Turkey.
If convicted, they risk life imprisonment, without the chance for parole. Due to the large number of defendants, they will appear before the court in groups.
The case is the first in which alleged members of al-Qaida are being tried by a court in this predominantly Muslim country with a staunchly secular state.
According to the 128-page indictment, Habib Akdas, the suspected leader of the cell, and two alleged cell members, Baki Yigit and Adnan Ersoz, met on several occasions with Abu Hafiz al-Masri, a former top lieutenant of Usama bin Ladin.
Al-Masri is believed to have arranged for Akdas and Yigit to meet bin Ladin in 2001 in Afghanistan. Al-Masri, alias Muhammad Atif, was killed in a US airstrike in Afghanistan in November 2001.
A total of 61 people were killed
in the November attacks
Yigit, who is in custody, said the Turkish cell initially proposed
kidnapping members of a pro-Western Turkish business group, but the idea was rejected by bin Ladin and al-Masri, the indictment said.
Instead, al-Masri and bin Ladin suggested attacks against Incirlik Air Base, a southern Turkish air base used by the US military, as well as against Israeli ships in the southern port of Mersin, the indictment said.
Intelligence officials have said the suspects ended up changing their targets because of high security at the sites.
Similar to treason
They asked for US$150,000 for the operation from al-Masri and the money was paid to the cell last year by affiliates in Europe and Iran, prosecutors said.
Prosecutors are demanding life sentences for suspected al-Qaida members Fevzi Yitiz and Usman Eken, who allegedly helped make the bombs;
Harun Ilhan, who allegedly helped recruit members of the cell; Ersoz, who allegedly helped arrange financing for the attacks; and Yusuf Polat, who allegedly kept watch at one of the bombed synagogues and gave the final go-ahead for the attack.
The five men are charged with a crime similar to treason.
The other 64 are charged with crimes such as membership in an illegal group or "aiding terrorists". Alleged ringleaders Akdas, Gurcan Bac and Azad Ekinci are at large and are believed to be hiding abroad.