Security services detained the Egyptian Initiative for Personal Rights (EIPR) workers, including director Gasser Abdel Razek, after the group gave a briefing to senior diplomats on 3 November.
The detentions, on charges including joining a terrorist group and publishing false news, drew public objections from the United Nations and Western governments, and triggered a broad campaign by international rights campaigners.
Abdel Razek, along with EIPR criminal justice director Karim Ennarah and administrative manager Mohamed Basheer were released on Thursday evening from Tora prison in southern Cairo, EIPR said.
A security source said earlier that the three would be released pending further investigations. There was no immediate official statement from the prosecution.
It was not immediately clear if the release meant charges against the three had been dropped.
Those who voiced concern about the arrests include Antony Blinken, who has been named as US president-elect Joe Biden's secretary of state, and Hollywood actress Scarlett Johansson.
Critics saw the arrests as the latest escalation of a crackdown on political dissent and civil society that has gradually tightened under president Abdel Fattah al-Sisi.
Independent local rights groups have largely stopped operating.
The 18-year-old EIPR is the most prominent group of the few who are still active, continuing to work on documenting civil rights violations, prison conditions, sectarian violence and discrimination against women and religious minorities.
Mr Sisi has said there are no political prisoners in Egypt, and that stability and security are paramount.
Additional reporting by agencies