They face a range of charges including being a member of a terrorist organisation, illegal possession of hazardous material and terrorist propaganda, Hurriyet newspaper reported, quoting the indictment.
The suspects face between three and 58 years in prison if convicted.
The June demonstrations began as a protest against the planned destruction of an Istanbul park known as Gezi but snowballed into a nationwide outpouring of anger against Prime Minister Recep Tayyip Erdogan's rule.
"Protests that began in May went beyond a democratic reaction and turned into propaganda and demonstration outlets of terrorist organisations with the guidance of marginal groups," the indictment said.
"As a result, public property was destroyed, civil servants were incapacitated and security forces were injured."
It was not clear whether those indicted on Friday were among 255 people who were also charged in December over the unrest.
Europe's top human rights organization on Tuesday slammed Turkey's crackdown on anti-government demonstrations earlier this year, saying its handling of the protests was proof of a "serious human rights problem" among the police.
Although Turkey had made "important progress in the fight against torture and ill-treatment" the treatment of protesters in Gezi Park underscored the "police's systemic problem of insufficient respect for binding human rights standards," the Council of Europe's Commissioner for Human Rights, Nils Muiznieks, said.
Muiznieks visited Turkey in July, after weeks of protests that rocked the country.
In a statement accompanying his report on his findings he pointed to "serious, consistent and credible allegations of excessive use of force, in particular excessive and improper use of tear gas and ill-treatment."
The commissioner also expressed concern about the punitive action taken towards some health workers, lawyers, academics, students and journalists for non-violent actions during the Gezi protests.
Some were placed under investigation while others were fined or dismissed.
"I am particularly worried about the chilling effect that these measures could have on free assembly and expression, as well as on media freedom," Muiznieks said.
The protests began in May over the government's plans to develop Istanbul's Gezi Park into a complex with new mosque and shopping centre. The excessive use of police force further enraged the protesters, who accused Prime Minister Recep Tayyip Erdogan of authoritarianism.
To protest the crackdown the European Union delayed a new round of membership talks with Turkey. The talks eventually began in November.
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