An Egyptian court on Tuesday convicted and sentenced to jail 43 nonprofit workers, including 16 Americans, in a case that has alarmed democracy advocates who fear a shrinking space for civil society more than two years after the country’s revolution.

The convictions, on charges of using foreign funds to foment unrest, threaten to further strain ties between Egypt’s fledgling government and Washington, which has criticized the crackdown on rights workers and assailed Tuesday’s verdict.

The majority of those convicted were given five-year prison terms, but they were tried in absentia, having already left Egypt. They are unlikely to return. Eleven others received a suspended sentence of one year.

But a handful faced the prospect of jail. Robert Becker, a former employee of the National Democratic Institute (NDI), was the only American defendant who stayed back in Egypt. Becker, who said he remained out of a sense of solidarity with the Egyptians who were charged, was given a two-year sentence.

On Monday, Becker wrote on his blog that he would defy his lawyer by staying in Egypt for the verdict. “I was told it would be best for me to go home, so that is exactly where I will be . . . home, in Cairo,” he wrote.

But late Tuesday evening, about 11 hours after the verdict was read, Becker announced on Twitter that he had “unwillingly and angrily gone into exile until appeals get sorted out.”

Becker, who has said the NDI fired him for his decision to remain in Egypt, has consistently maintained that he and his colleagues are innocent.

Nancy Okail, who directed operations in Egypt for Freedom House and was convicted in absentia Tuesday, called the verdict “the worst that could have happened. The crime that we committed was to work on human rights and democracy.”

The case against the 43 workers has its roots in a December 2011 raid on the Cairo offices of multiple nonprofit organizations, including several prominent U.S.-based groups: the NDI, the International Republican Institute (IRI) and Freedom House. The government said the groups were trying to foment unrest — a dubious charge given that they were operating openly and in cooperation with the government.

At the time, Egypt was being run by the military council that filled the void after President Hosni Mubarak was forced to resign in February 2011. But the prosecutions have persisted under elected President Mohamed Morsi, who has come under increasing fire for what critics claim are authoritarian tendencies.

Last week, Morsi submitted a bill to parliament that rights groups say would curtail their ability to operate in Egypt. Although Egypt’s judiciary is constitutionally separate from the
Morsi-run executive branch, rights advocates say Tuesday’s verdict, coupled with the proposed law, will have a chilling effect on their operations.

“This is a message meant to intimidate the NGOs,” or nongovernmental organizations, said Mamdouh Nakhla, chairman of the al-Kalema Center for Human Rights, a small advocacy organization. “Morsi doesn’t want scrutiny of his actions. He doesn’t want pressure from all these groups.”

In particular, Nakhla said, he is concerned by a provision of the proposed law that would allow a committee to vet a nonprofit group’s funding sources. With Morsi’s Muslim Brotherhood backers and other Islamists firmly in control of the government,
Nakhla said he fears that secular groups will be targeted.

Kamal Nour El Din, a member of the Brotherhood’s Freedom and Justice Party who chairs the parliamentary committee responsible for the new legislation, said critics have misinterpreted the proposed law. The goal, he said, is simply to streamline a process that had long been considered mystifyingly bureaucratic.

It is unclear when, or even whether, the legislation will be taken up for a vote. Egypt’s lower house of parliament has been disbanded, and the law governing the remaining upper house was ruled invalid Sunday by the nation’s supreme court. The court said the upper house, known as the Shura Council, can continue to operate pending new elections, a date for which has not been set.

None of the 43 defendants appeared to be in the Cairo courtroom Tuesday, where a three-judge panel also ordered the shuttering of the local branches of the workers’ employers: the IRI, the NDI, Freedom House, the International Center for Journalists and Germany’s Konrad Adenauer Foundation.

In a statement, the IRI called the case “politically motivated.”

“Today’s ruling will have a chilling effect on Egyptian civil society and, taken with other recent developments, raises serious questions about Egypt’s commitment to the democratic transition that so many people demanded when they took to the streets in early 2011,” the statement said.

The White House said in a statement that the United States is “deeply concerned” by the verdict in what it called a politically motivated trial. “The court’s decision undermines the protection of universal human rights and calls into question the Government of Egypt’s commitments to support the important role of civil society,” it said.

Among those sentenced in absentia was Sam LaHood, son of U.S. Transportation Secretary Ray LaHood. The younger LaHood had led the IRI’s operations in Egypt but was forced, along with others, to hide in the U.S. Embassy for a month in early 2012 until he was permitted to leave the country.

Lara El Gibaly contributed to this report.