A sudden and sweeping halt to U.S. foreign aid by the Trump administration does not apply to weapons support to Israel and Egypt and emergency food assistance, according to a memo issued by the department to bureaus and U.S. missions overseas on Friday.

The same day, the White House told the Pentagon it could proceed with a shipment of 2,000-pound bombs to Israel that President Biden abruptly halted last summer to try to dissuade the Israeli military from destroying much of the city of Rafah. Israeli forces went ahead with bombing the city.

The shipment has 1,800 MK-84 bombs, said a White House official who agreed to discuss sensitive weapons aid on the condition of anonymity. Such bombs are judged by U.S. military officers to be generally too lethal and destructive for urban combat. Until the halt, the Biden administration had shipped the bombs to Israel as its military fought Hamas in Gaza.

The memo on foreign aid was sent by Secretary of State Marco Rubio and lays out how the State Department, the linked United States Agency for International Development, or U.S.A.I.D., and other agencies are expected to execute an executive order halting foreign aid during a 90-day reassessment period. President Trump signed the executive order on Monday, soon after his inauguration.

The memo requires any employee working on foreign aid to refrain from designating new funding and taking applications, and to issue “stop-work” orders to groups that have received grants. The memo has circulated online and has ignited panic among groups around the world that rely on foreign aid from the United States for their programs — which range from disease prevention to curbing infant mortality to alleviating the impact of climate change.

Some groups say they will likely stop work immediately and begin laying off employees or suspending salaries.

The State Department also oversees military aid to allies and partner nations. A line in the memo specifically exempts Israel and Egypt and any salaries paid to people who manage that aid. Both nations receive foreign military financing, which is direct money from the U.S. government for them to purchase weapons and other military equipment. They then use that money to buy arms and equipment from U.S. weapons makers, as well as to pay for military training.

The halt to foreign aid applies to military assistance to Ukraine, Taiwan, Lebanon and other partner nations, including members of NATO. Much of the recent urgent aid for Ukraine in its defensive war against Russia has been sent out already. Officials in the Biden administration anticipated that Mr. Trump would try to halt arms aid to Ukraine since he had expressed skepticism about it. Mr. Rubio was one of 15 Republican senators who voted last April against legislation centered on weapons aid to Ukraine.

The State Department did not have an immediate response when asked to comment for this story.

Military support of Israel has become a divisive issue in the United States. Israel’s devastating strikes against Palestinians in Gaza, mostly using American bombs, since Hamas attacked Israel in October 2023 have galvanized widespread criticism of the decadeslong bipartisan policy of sending military aid to Israel. Former President Joseph R. Biden Jr. approved $26 billion in military aid to Israel after the war began, and Mr. Trump has said he intends to continue supporting Israel.

Some lawmakers, particularly Democrats, also criticize the long-running U.S. policy of giving substantial arms aid to Egypt. Last year, Congress approved $1.3 billion of military aid to Egypt, but said $320 million would be conditioned on a review by the State Department of whether Egypt had improved practices around human rights. Last September, the secretary of state, Antony J. Blinken, approved that entire amount, despite persistent criticism of Egypt’s human rights record from some Democratic lawmakers and watchdog groups.

The State Department memo also orders officials to set up a central repository or database of all foreign aid given out by the U.S. government, and it says all aid must be reviewed and approved by Mr. Rubio or people whom he designates with approval authority. This is to ensure that aid is “in keeping with one voice of American foreign policy.” People who have seen the memo confirmed its authenticity to The New York Times.

The memo says the director of the office of policy planning in the department will develop guidelines for review of all foreign aid within 30 days. The director is Michael Anton, who worked on the National Security Council in the first Trump administration. Mr. Anton is known for writings that include a 2016 essay, “The Flight 93 Election,” that said conservatives must take radical action to remake America in their vision rather than stick with the status quo.