The 26 members of the Taksim Solidarity Platform each faced up to 29 years in prison on charges including founding a crime syndicate, violating public order and organising illegal protests through social media.
The group includes prominent civil society figures and was the leading organisation behind last June's protests that left six people dead.
But the court rejected the six-page indictment prepared by the Istanbul prosecutor's office, saying it was unclear which laws the suspects had violated, Radikal newspaper reported.
"It should be explained how some of the suspects founded and controlled an organisation to commit which crimes, under which law, so as to permit them to defend themselves," the court was quoted as saying.
Last month, Turkish prosecutors charged another group of 36 protesters with terrorism, and demanded prison terms ranging up to 58 years.
The June protests started as a small environmentalist movement to save Istanbul's Gezi Park from redevelopment and snowballed into a nationwide wave of protests against Erdogan, who is accused of increasing authoritarianism.