By DAVID D. KIRKPATRICK and STEVEN LEE MYERS
CAIRO — Security forces shut down three American-financed democracy-building groups and as many as six other nonprofit organizations on Thursday, in a crackdown that signaled a new low in relations between Washington and Egypt's military rulers.
Two of the organizations, the National Democratic Institute and the International Republican Institute, had been formally authorized by the Egyptian government to monitor the parliamentary elections set to resume next week. Critics said the surprise raids contradicted the military's pledge to hold a fair and transparent vote.
The other American-financed pro-democracy group whose offices were closed, the advocacy group Freedom House, had completed its application for official recognition just three days ago. An American group that helps train Egyptian journalists was among the other nonprofit groups raided.
Human rights activists said security forces barging into the offices of respected international organizations was unprecedented, even under the police state of President Hosni Mubarak, who was ousted this year.
The raids are the latest and most forceful effort yet by the country's ruling generals to crack down on perceived sources of criticism amid rising calls from Egyptian politicians and protesters and some Western leaders for the military to hand over power to a civilian government. Those calls were punctuated by Secretary of State Hillary Rodham Clinton's expression of outrage last week over the military's beating and stripping of female demonstrators in Tahrir Square.
On Thursday, a State Department spokeswoman announced that it was "deeply concerned" by the raids.
"Suffice it to say we don't think that this action is justified," the spokeswoman, Victoria Nuland, said. "We want to see the harassment end," she added, calling the raids "inconsistent with the bilateral cooperation we've had over many years."
Another senior administration official, speaking on the condition of anonymity, said that in private channels, the United States had sent an even stronger message: "This crosses a line."
"It's triggered by ongoing concerns about control," the official added, as the ruling military council confronted the mounting pressure to hand over power.
Others called the raids a major challenge to Washington's policy toward Egypt, which receives $1.3 billion a year in American military aid.
"It is a major escalation in the Egyptian government's crackdown on civil society organizations, and it is unprecedented in its attack on international organizations like Freedom House, which is funded in large part by the United States government," said Charles Dunne, director of Middle East and North Africa Programs at the organization, which advocates democratic reforms. "The military council is saying we are happy to take your $1.3 billion a year, but we are not happy when you do things like defending human rights and supporting democracy."
The state news media said that the raids were part of an investigation into what it described as illegal foreign financing.
Contingents of soldiers and security officers armed with automatic weapons and wearing bulletproof vests burst into the offices of the nonprofit organizations at roughly the same time Thursday, around 1 p.m.
The officers provided no warrants or explanations, according to officials at several of the groups. They detained the groups' employees inside for more than five hours in some places. The security forces collected stacks of binders and files, confiscated computers, and sealed the doors as they left.
At the National Democratic Institute's office in Cairo, armed men in uniforms and plain clothes could be seen through a locked gate slicing open boxes of files stacked in a garage.
"Nobody understands what's going on," said Belal Mostafa Gooda, an Egyptian employee of the National Democratic Institute, in a furtive phone call from inside its locked gate during the raid. "We can't move inside or go outside," he said, adding, "They're searching all the papers and files and all laptops, and we don't know what will happen."
The National Democratic Institute receives United States government financing, promotes democracy abroad and says it is loosely affiliated with the Democratic Party. The International Republican Institute also receives government money, and is affiliated with some prominent Republicans.
The raids hit at least one German democracy-building group. The security forces also struck the Egyptian Budgetary and Human Rights Observatory, which studies the military and its spending. The officers also shut down an organization that argues for judicial independence.
Egyptian human rights groups are almost completely dependent on foreign financing because the hostility of the Mubarak government scared away Egyptian donors, and many received considerable support from the European Union as well as the United States.
But Egypt's military rulers began railing against the dangers of foreign financing to Egyptian sovereignty around the time last spring that the United States said it would allocate $65 million to help foster electoral democracy here. Although the United States is Egypt's most important benefactor, its policies in the region are also very unpopular here, making it an easy target.
Egyptian state news media have made it clear since the military-led government began investigating allegations of improper financing months ago that its principal target was money from the United States; in the most notable instance, a state-owned magazine greeted the new American ambassador, Anne W. Patterson, a few months ago with a cartoon cover depicting her holding wads of burning cash in the middle of Tahrir Square. "Ambassador from Hell," read the caption.
As new clashes have broken out between the military police and protesters challenging military rule — more than 80 have died since October — the generals have often warned that there are "hidden hands" trying to stir up trouble or "bring down the state." They have increasingly suggested that those hidden hands could be foreign-financed.
In a television interview last month, Maj. Gen. Mamdouh Shaheen suggested several times that the investigation into foreign financing of nongovernment organizations would shed light on the unnamed instigators who he said were behind the protests and clashes in the streets.
"There are hidden hands playing in the country," he said. "We tell the Egyptian people, and the Egyptian people are smart, that there are people who are trying to demolish the country."
Most human rights and democracy groups in Egypt already operate in a legal twilight because of Mubarak-era laws allowing only nongovernment organizations licensed by the government. Before and after his ouster, the Egyptian government has seldom granted such licenses to genuinely independent organizations.
"We are in the same gray zone everybody else is," said Heba Morayef, a researcher with Human Rights Watch here, a group that was not raided. "We are not licensed and we can be shut down and jailed and all of that, but we keep the authorities informed." After the revolution, she said, most such groups expected their lot to improve: "I don't think anybody expected there would be a new crackdown."