The trial, which began in late February, was the culmination of the worst and most public spat between Washington and Cairo in decades.
Closed-door negotiations to avert a crisis ended with most of the American defendants being allowed to leave when a travel ban was lifted in March, but the trial of Egyptian defendants and one American who elected to remain behind continues.
Another Egyptian-American dual national defendant returned to observe the trial and was detained Sunday at Cairo airport. But the court ordered former Freedom House employee Sherif Mansour, who appeared at the court Tuesday wearing handcuffs, to be freed until the verdict. A German defendant also joined the case on Tuesday.
Some 43 defendants, including 16 Americans, face charges of operating groups and receiving funds without permits. Only 17 defendants appeared in courts Tuesday.
The U.S. issued a harsh denunciation of the trial late Monday, calling it "politically motivated."
State Department spokesman Mark Toney urged Egyptian authorities "to stop trying these individuals and instead resolve any outstanding issues that they may have on this matter in a government-to-government basis," pledging to continue to work with civil society as "an important component to a successful democratic transition for Egypt."
Court sessions so far have been largely procedural.
The case began when Egyptian security raided the offices of a number of pro-democracy groups, including four American ones—the International Republican Institute, the National Democratic Institute, Freedom House and a group that trains journalists.
Last December, officials said the groups were suspected of accepting foreign funds to stir up unrest.
Rawda Saeed, one of the defendants in court Tuesday, said prosecution witnesses including Egypt's Minister of International Cooperation Fayza Abolnaga will address the court starting July 4.
Abolnaga, a minister since 2001 during the regime of Hosni Mubarak, was one of the main plaintiffs against the groups. She filed reports to authorities about their alleged illegal receipt of foreign funds and made media appearances denouncing the threat she claimed they posed.
The law regulating receipt of foreign funds dates from Mubarak's presidency. He was deposed in a popular uprising in February 2011.
Tuesday's session was the fifth since the trial began late February, and the case has not yet started in earnest.
"Slow justice is not justice," Saeed said. "We haven't even started a defense. This is driving us all crazy."