A file photo of the U.S. embassy in downtown Cairo,...

A file photo of the U.S. embassy in downtown Cairo, Egypt. (Aug. 14, 1998) Credit: AP

Three American citizens barred from leaving Egypt have sought refuge at the American Embassy in Cairo amid growing tensions between the two allies over an Egyptian investigation into foreign-funded pro-democracy groups.

The White House said Monday it was disappointed with Egypt's handing of the issue, which U.S. officials have warned could stand in the way of more than $1 billion in badly needed U.S. aid.

The growing spat between the two longtime allies reflects the uncertainty as they redefine their relationship nearly one year after the ouster of President Hosni Mubarak following an 18-day popular uprising.

Mubarak was a steadfast U.S. ally, scrupulously maintaining Egypt's peace treaty with Israel and while seeking to mediate between Israel and the Palestinians — a clear American interest.

Now, Egypt's council of ruling generals, who took power when Mubarak stood down last Feb. 11, often accuse "foreign hands" of promoting protests against their rule.

At the same time, members of Egypt's Muslim Brotherhood, which dominates the new parliament, have suggested that they could seek to re-negotiate parts of the 1979 Israel-Egypt peace treaty, causing alarm in Israel and concern in Washington over the possibility that Egypt will no longer serve as its solid anchor in the Middle East.

Egypt's investigation into foreign-funded organizations burst into view last month when heavily armed security forces raided 17 offices belonging to 10 pro-democracy and human rights groups, some U.S.-based. U.S. and U.N. officials blasted the raids, which Egyptian officials defended as part of a legitimate investigation into the groups' work and finances.

Last week Egypt barred at least six Americans and four Europeans who worked for U.S.-based organizations from leaving the country. They included 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 only Republican in President Barack Obama's Cabinet.

On Monday, U.S. State Department spokeswoman Victoria Nuland told reporters in Washington that some of the Americans under investigation were in the embassy, although she would not identify them or their affiliations, citing privacy concerns.

"We can confirm that a handful of U.S. citizens have opted to stay on the embassy compound in Cairo while awaiting permission to depart Egypt," she said.

Nuland added that those seeking refuge in the embassy were not "seeking to avoid any kind of judicial process," noting they had been interrogated before.

The U.S. Foreign Affairs Manual states that such request for refuge are generally granted only when the U.S. citizen "would otherwise be in danger of serious harm."

Another U.S. official, speaking on condition of anonymity because of the sensitivity of the issue, said three Americans were at the embassy.

It was unclear if LaHood was among them. In a text message, LaHood referred queries to an IRI spokeswoman in Washington, who did not respond to requests for comment. LaHood said last week that he had been told by his lawyer that he was under investigation on suspicion of managing an unregistered NGO and receiving "funds" from an unregistered NGO — namely, his salary.

White House spokesman Jay Carney said the U.S. had been in touch with Egyptian officials about the issue.

"We've made clear our concerns about this issue and our disappointment that these several citizens are not being allowed to depart Egypt," he told reporters in Washington Monday. Last week, Obama discussed the issue by phone with Egyptian military chief Field Marshal Hussein Tantawi.

U.S. officials have warned that restrictions on civil society groups could hinder aid to Egypt, funds the country badly needs given the severe blows continued unrest has dealt its economy over the last year.

The U.S. is due to give $1.3 billion in military assistance and $250 million in economic aid to Egypt in 2012. Washington has given Egypt an average of $2 billion in economic and military aid a year since 1979, according to the Congressional Research Service.

Recent U.S. legislation conditions the continuation of that aid on Egypt's taking certain steps in its transition to democracy. These include abiding by its 1979 peace treaty with Israel, holding free and fair elections and "implementing policies to protect freedom of expression, association and religion and due process of law."

The new strain on the U.S.-Egypt relationship underlines the wider question of where the various groups struggling for power will lead the country. For months, the ruling military council has faced frequent protests over its handling of the transition and calling for it to immediately hand over power to civilians.

Military leaders have blamed unidentified "foreign hands" for these demonstrations, saying they sought to destabilize Egypt.

On Monday, a member of the civilian panel created by the military to advise it said the army was considering ways to speed up the transition.

As a sign, however, that U.S.-Egypt military cooperation will continue, a delegation from Egypt's Defense Ministry arrived in New York Sunday. Egypt's state news agency quoted military attache Gen. Mohammed el-Kishki as saying that the delegation would visit U.S. military bases, meet with members of Congress and discuss bilateral military cooperation.

It remains unclear how many foreigners have been barred from leaving Egypt.

LaHood said last week that three other employees of his organization were on the no-fly list, two Americans and one European.

From the National Democratic Institute, which was also raided in December, three Americans and three Serb employees are on the list, the group's Egypt director, Lisa Hughes, said last week.

Hughes said in a text message Monday that none of NDI's employees are staying at the U.S. Embassy.

A U.S. Embassy spokeswoman did not respond Monday to requests for comment.

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