By DAVID D. KIRKPATRICK and J. DAVID GOODMAN

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 organizatio