The IBDA-C claimed joint responsibility with al-Qaeda for two bombings at Istanbul synagogues and attacks on a British consulate and HSBC bank in November 2003.
The Sunni Muslim group, which seeks to create an Islamic state in Turkey, has been placed on the European Union’s terrorist list.
The police raided places in the cities of Istanbul, Ankara and the western province of Izmir after a year-long investigation.
No plans or information were found to suggest an attack was being planned against Pope Benedict whose recent historic trip to Turkey was his first official visit to a Muslim country and was seen as a bid to improve relations between Christians and Muslims.
Several al-Qaeda-linked detentions during the Pope's visit were made according to sources.
Turkey, which has a 99 per cent Muslim population, has arrested several al-Qaeda suspects in recent years.