CAIRO — The USAID director in Egypt abruptly flew back to Washington on Thursday after less than a year on the job, the first major casualty of a row between the two longtime allies over American funding for pro-democracy groups. Jim Bever left his post the day after the Obama administration chastised Egypt's leaders for stoking anti-American sentiment during the country's rocky transition to democracy. In the rare public rebuke, the U.S. said it had noticed mounting attacks and criticism of U.S. aid and motives. A U.S. Embassy statement said Bever will be "returning to Washington to take on new responsibilities and prepare for his next deployment." It did not say why his tour was cut short. The criticism of the U.S. is a sign that Egypt's military rulers are growing anxious over foreign aid they fear could strengthen the liberal groups behind Egypt's uprising at the expense of the military's own vast power. Those youthful, pro-democracy groups have grown more critical of the ruling generals lately over what they see as the slow pace of the transition away from authoritarian rule. Bever has been at the center of a dispute over funding since March, when USAID — the American government organization that distributes international development aid — placed advertisements inviting non-governmental groups in Egypt to apply for U.S. funding. The ads attracted hundreds of applicants, who lined up outside USAID offices in a quiet suburb south of Cairo. Over the next few months, the American aid organization allocated millions of dollars to the groups. This left the government seething. It insisted that the funding must go through official channels, and not directly to the groups. Those restrictions applied during the rule of ousted President Hosni Mubarak, whose government tightly controlled the process. Last month, Maj. Gen. Mohammed al-Assar, a member of the Supreme Council of the Armed Forces, gave a speech in Washington and criticized the United States for funding pro-democracy groups without submitting to Egyptian government supervision. He said it violated Egyptian laws for funding non-governmental organizations. "It is a matter of sovereignty," he said. Elizabeth Colton, spokeswoman for the American Embassy in Egypt, told The Associated Press on Thursday that the U.S. is not interfering in Egypt's politics. "Egyptian groups that apply for and receive grants from the United States are engaged in activities that are politically neutral. No funds are provided to political parties," she said. Egyptian authorities this week opened a formal investigation into the funding issue, according to a judicial official involved in the process. "A list of the likely beneficiaries of American funding has been compiled and we will investigate them one by one," said the official, who spoke on condition of anonymity because the investigation was in its early stages. Other generals on the ruling council have accused two key reform groups of following a "foreign agenda" and of receiving funding and training from abroad, claims that suggest plotting against the country with foreign help. The activist groups April 6 and Kefaya, Arabic for "Enough," fought back by lodging official complaints with the prosecutor's office against Maj. Gen. Hassan el-Roweini, the ruling council member who made the accusations. April 6 is also demanding an apology. Kefaya and April 6, which both called for Mubarak's ouster years before the uprising, are credited with key roles in organizing the protests that toppled the president. Claims of a "meddling foreign hand" have routinely found resonance among Egyptians. More than a few are convinced that the United States, Israel and others are constantly scheming against their nation and Islam, the faith of most Egyptians. Amid all the xenophobia, anti-American sentiments have stood out. The July 31 issue of a state-run magazine featured a cover depicting new U.S. Ambassador Anne Patterson as holding a burning wad of dollars to the wick of a bomb wrapped in an American flag. The headline read: "The ambassador from Hell who lit a fire in Tahrir." The U.S. State Department on Wednesday complained that the criticism was "inaccurate" and "unfair" and that personal attacks against Patterson were "unacceptable." Still the U.S.-Egypt row is not likely to cause lasting harm to relations. Egypt's military and the U.S. government are bound by close links going back to the 1970s. The military has for more than 30 years received about $1.3 billion in annual U.S. assistance and frequently staged joint war games with U.S. forces. Egyptian generals regularly travel to Washington for extended visits for talks with their American counterparts and visit military facilities. Responding to criticism in the local media of the U.S. policy on funding non-governmental groups in Egypt, former U.S. Ambassador in Egypt Margaret Scobey suggested that the methods of the ruling generals were not much different from those of Mubarak. "In the Mubarak era, this assistance was often labeled 'interference', and opposed by a government uncomfortable with hearing the voices of its own people," she wrote several months ago.