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“We are doing our best to contain this but … we cannot actually exercise any influence on the investigating judges right now when it comes to the investigation,” Mr. Amr told reporters.

He insisted that “the executive branch has nothing to do” with the investigation.

Among the Americans barred from leaving Egypt is Sam LaHood, the head of the Egypt office of the Washington-based International Republican Institute and the son of U.S. Transportation Secretary Ray LaHood.

The ban came as part of Egypt‘s investigation into foreign-funded organizations blamed for fueling street protests.

“We are very clear that there are problems that arise from this situation that can impact all the rest of our relationship with Egypt,” Mrs. Clinton told reporters in Germany. “We do not want that. We have worked very hard this past year to put in place financial assistance and other support for the economic and political reforms that are occurring in Egypt.”

Under U.S. law, Mrs. Clinton must certify to Congress that Egypt is meeting certain requirements, including enacting democratic and rule of law reforms, in order for the assistance to be released.

With the U.S. voicing concerns about the NGO workers and the military’s commitment to democratic reform, it could call into question additional funding sources from the European Union, for example, which also wants to see Egypt makes democratic reform strides and commitments.

AP writer Tarek El-Tablawy contributed to this report.