Kenneth Roth, executive director of the New York-based NGO, and HRW Middle East director Sarah Leah Whitson were held overnight in Cairo airport before being denied entry, Whitson wrote on Twitter.
"It's official - shortest visit to Cairo ever - 12 hours before deportation for 'security reasons'- the new Egypt certainly 'transitioning'," Whitson wrote.
The rights activists had flown to Cairo for the release of a report to mark a year since the mass killing of an estimated 700 opposition protesters, in one of the deadliest incidents of its kind in decades.
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The protesters, supporters of deposed Islamist president Mohamed Morsi, had been camped out around the Rabaa al-Adawiya mosque in Cairo for weeks when police moved in to disperse them on August 14, using tear gas and live ammunition.
A government official estimated roughly 700 protesters were killed in the dispersal, along with eight policemen.
Rights activists say the number of dead could have been significantly higher.
"Rab'a massacre numbers rank with Tiananmen and Andijan but Egypt gov't wouldn't let me in to present report on it," Kenneth Roth wrote on Twitter.