An Egyptian court on Tuesday handed down prison sentences to 43 activists, 16 of them Americans, including the son of the U.S. Secretary of Transportation, in a case against foreign-funded pro-democracy groups.

Except one, all the Americans, including Sam LaHood, son of the U.S. Transportation Secretary Ray LaHood, were sentenced in absentia because they were no longer in Egypt. LaHood and 26 others received a five-year jail term while another five were handed down two-year sentences and the remaining 11, all of them Egyptian, faced lesser charges and were given one-year suspended prison sentences.

Robert Becker, the lone American defendant who was in Egypt during the trial, left the country for Rome on Tuesday, shortly after the verdict was pronounced, AP reported citing a Cairo airport official, who spoke on condition of anonymity.

Becker said he had remained in Egypt to show solidarity with other Egyptian defendants, the report added.

The court also ordered the shutdown of Egyptian operations of the U.S.-based International Republican Institute (IRI), National Democratic Institute (NDI) and Freedom House, among others, involved in the case.

The U.S. denounced the verdict and expressed deep concern over the guilty verdicts and sentences, calling the trial “politically-motivated.”

U.S. Secretary of State John Kerry said the sentencing, as well as Egypt’s decision “to close these organizations’ offices and seize their assets contradicts the Government of Egypt's commitments to support the role of civil society as a fundamental actor in a democracy and contributor to development, especially at this critical stage in the Egyptian people's democratic transition.”

In July 2011, Egypt began a crackdown on nonprofit organizations, some of which were foreign-funded and had a number of U.S. representatives.

In December 2011, Egyptian authorities raided seven international and Egyptian NGOs, and in February 2012, charters were filed against 43 nonprofit workers, including Americans, Europeans, Egyptians and other Arab nationals.

Egyptian prosecutors investigated charges that the groups lacked necessary government approvals and they received overseas funds illegally.

U.S. State Department spokesperson Jen Psaki said Washington would take up the issue with Egyptian officials, and added that Cairo “should resolve outstanding issues with the United States on a government to government basis.”

Three senior Republican senators -- John McCain, Lindsey Graham and Kelly Ayotte -- said the verdict will “significantly” affect Washington's relations with Cairo, AP reported.

The verdict came a week after Egyptian President Mohamed Morsi proposed a bill to regulate non-profits, after previous drafts drew criticism that they would let security services gain control over non-profit groups.

Morsi’s office said the new proposal would use provisions within Egyptian law to regulate foreign funding of non-profits, but critics said the new draft did not allow nonprofits to function independently and failed to allow them to secure funding to survive.