Turkey director Idil Eser was detained on July 5 along with seven other activists and two foreign trainers during a digital security and information management workshop on Buyukada, an island south of Istanbul.
"Six were remanded in custody and four released on judicial control," Amnesty International's Turkey researcher Andrew Gardner told AFP.
Prosecutors accuse them of "committing a crime in the name of a terror organisation without being a member," he said.
Their detention sparked international alarm and amplified fears of declining freedom of expression under President Recep Tayyip Erdogan.
The ruling came a day after the activists, who have not yet been put on trial or formally charged, gave statements to prosecutors for the first time since their detention.
Relatives of the activists, who gathered outside the Istanbul courthouse Monday, looked worried and refused to speak to journalists.
Eight of those detained were Turkish rights activists, including Ilknur Ustun of the Women's Coalition and Veli Acu of the Human Rights Agenda Association. Four of those have now been released, Gardner said.
Two foreigners - a German and a Swedish national who were leading the digital information workshop - remain in pre-trial detention.
Speaking to journalists outside the Istanbul court ahead of the ruling, Gardner said if the activists were remanded in pre-trial prison custody, "that would be a travesty of justice," and called for their immediate release.
"This is a test for Turkey's judiciary," he said.
"Turkey will be disgraced in the eyes of the world if these human rights defenders are put in prison for defending human rights."
President Recep Tayyip Erdogan said this month that the activists were detained on a tip-off they were working against the government, comparing them to those involved in a failed putsch in July last year.
Gardner said the meeting on Buyukada had been a "routine" workshop and there was nothing suspicious about it.
"What is absolutely crystal clear, one hundred percent clear is this was a routine human rights workshop -- the sort of workshop that happens all over Turkey, in fact the sort of workshop that happens all over the world," he said.
Gardner said before the court ruling that country director Eser remained "in good spirits."
"She sent messages that as soon as she is released she wants to carry on from where she left off," he said.
Amnesty International's Turkey chair Taner Kilic was last month also arrested, accused of links to US-based preacher Fethullah Gulen, who is accused of ordering last year's failed coup, a charge he denies.