U.S. relations with Egypt's ruling military have turned prickly in the dispute over Egypt's clampdown on pro-democracy, non-governmental organizations.

Cairo authorities, amid allegations that foreign NGOs have been fomenting clashes between political activists and military government authorities in the country, has banned some 40 foreign NGO personnel from leaving the country and appears ready to prosecute them for violating Egyptian laws.

Nineteen of those banned are U.S. citizens and the administration of U.S. President Barack Obama, as well as members of Congress, have protested the action and demanded those detained be allowed to leave, if they so wish.

At stake, they warn, is the $1.3 billion in annual aid the United States has provided Egypt's military since Egypt signed the U.S.-sponsored Camp David Accords with Israel in 1978. Also at stake is about $250 million in economic aid and possible U.S. support for International Monetary Fund assistance to Egypt, whose revenues have fallen since the ouster last year of President Hosni Mubarak, the street clashes that led to it and which continue.

"We are very clear that there are problems that arise from this situation and that can impact all the rest of our relationship with Egypt," U.S. Secretary of State Hillary Clinton said.

Added White House spokesman Jay Carney, "These actions have consequences for our relationship and for our assistance programs."

Military authorities in Cairo, however, insist the matter is out of their hands. The NGOs hadn't properly registered with the government and received funds from abroad for their unsanctioned activities. It is a judicial matter, they have argued, and those involved as well as their organizations are under investigation.

And there the matter stands: Washington scowls over what it considers an affront to democratic rights in society; Cairo frowns, meanwhile, over what it sees as U.S. meddling in its domestic affairs.

It's not surprising ties between the United States and Egypt are under strain. Egypt under Mubarak and his authoritarian government was a vital U.S. ally in the region, a fact that the $1.3 billion in military aid underlined. But Arab Spring protests that erupted in Egypt appear to have caught the United States flat-footed and once it was clear Mubarak was as good as gone, Washington rushed to embrace the change despite the uncertainty of it.

Protesters in Cairo were hailed for their courage, their yearning for democracy. The military, which has assumed temporarily control of the country, was encouraged to set the stage for general elections, promote democratic reform and rule of law, which has not come fast enough for demonstrators in Cairo, who believe the military are dragging their feet on reforms to preserve their traditional place of power, nor for the U.S. Congress.

Legislation in the United States now makes it mandatory -- except for a strong, bona fide national security reason -- for the U.S. State Department to verify Egypt is making progress toward democracy for aid to continue.

Preliminary elections have been conducted, with the Islamist Muslim Brotherhood claiming the biggest share of the votes. Salafists (even more fundamentalist in their Islam) made a strong showing as well -- a fact that doesn't augur well for Egypt's future relations with Israel or the United States.

In the NGO confrontation, the Muslim Brotherhood has said the country's investigation of non-governmental organizations should take place. Not surprising as it moves toward what it sees as control of the government later this year and that participants in the demonstrations taking place in Cairo tend to be mainly secularists.

What next? Reports from Cairo indicate the country's military well step in and NGO staff members banned from travel will be allowed to leave. Such a move would calm the situation.

But with Egypt's political turmoil continuing and America's strategic interests in the country unchanged, Egyptian-U.S. ties remain in a state of flux and therefore uncertain. The current dispute may just be the beginning of a very rocky road ahead.