Turkish police were frantically searching for other suspects linked to the man, who had undergone plastic surgery apparently to help conceal his identity. Authorities were also hunting for two squads of possible suicide bombers, reports said.
Meanwhile, Israel lifted a travel warning against visiting southern Turkey that was in place because the apparent al Qaeda threat was against Israeli tourists.
A statement from Israel's counterterrorism center said that due to efforts from Turkey's security forces, the threat level had dropped.
Defense lawyer Osman Karahan said his client, who was identified in the Turkish press as Lu'ai Sakra, was found with 1,650 pounds of explosives.
"He was planning to hit Israeli ships in international waters with these explosives," CNN-Turk quoted Karahan as saying.
Sakra shouted that he had no regrets after he was led handcuffed by police into the courthouse.
"I was going to attack Israeli ships," he said. And then in an ominous threat, he added: "If they come, my friends will attack them."
"I had prepared a ton of explosives," he also said in a barely audible voice. He spoke Turkish with an Arabic accent.
A statement from police headquarters said the suspect had an important position within al Qaeda and had undergone plastic surgery. The Hurriyet newspaper said Sakra had had plastic surgery several times, to change his appearance.
A Turkish police official said security forces were looking for other suspects linked to Sakra. Private NTV television said police were searching for two teams of possible suicide bombers.
Five cruise ships carrying some 5,000 Israeli tourists have been diverted from Turkish ports to Cyprus in recent days following intelligence reports that a terror attack was imminent.
Israel on Monday urged its citizens not to visit beach resorts on Turkey's Mediterranean coast before reversing the travel warning Thursday. Turkey is a top vacation spot for Israelis, and more than 300,000 visit each year.
In Israel, a security official said the Israeli travel warning will remain in effect due to a continued threat of attack.
The Istanbul court charged Sakra Thursday with membership in an illegal organization, defense lawyer Ilhami Sayan said. He refused to give any details, citing court regulations.
A police official said Sakra was planning to attack Israeli cruise ships with Zodiac speedboats packed with explosives. The official spoke on condition of anonymity because only top-level officials are allowed to speak on the record without prior authorization.
As Sakra left the courthouse, he shouted: "I was planning an attack in open seas. Allahu akbar, Allahu akbar."
Sakra faces up to five years in prison if convicted of membership in an illegal organization.
Another Syrian, identified by the semiofficial Anatolia news agency as Hamed Obysi, whom Turkish reports said was an al Qaeda courier, was also charged Wednesday with membership in a terrorist organization.
Police said Sakra is believed to have acted as a contact between al Qaeda and Turkish extremists responsible for the 2003 bombings of two synagogues, the British Consulate and a British bank in Istanbul. The bombings killed some 60 people.
Sakra also is accused of helping the masterminds of those attacks flee the country. They reportedly fled to Iraq and joined the insurgency there.
Police believe Sakra was still in contact with al Qaeda operatives planning future attacks.
Suspects tried in Turkey for the 2003 Istanbul bombings said they originally were planning to attack an Israeli cruise ship in the Mediterranean, according to a court indictment.
Police said in a statement that the two Syrians were detained following an investigation into a fire that broke out in the early hours of Aug. 4 in a house in Antalya.
Bomb squad members and police intelligence officers were brought to the area after people noticed strong chemical smells coming from the house, the statement said.
Police apparently had been watching the two Syrians before the fire and later tied them to the house and the Istanbul bombings.
Last Saturday, police stopped Obysi after he tried to bribe border police to allow him to cross into Syria, the statement said.
Sakra was detained at an airport in the southern city of Diyarbakir carrying a false identity card, it added.
By C. Onur Ant