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The US State Department has ordered a freeze on almost all funding for foreign assistance programs, days after president Donald Trump issued an executive order to pause aid for 90 days.

The order from the State Department on Friday, accompanied by a memo from Secretary of State Marco Rubio, includes exceptions for emergency food programs and military aid to Israel and Egypt.

On Monday, the US president ordered a 90-day pause in foreign development assistance to review its efficiency and ensure it aligned with his foreign policy.

The memo from Mr Rubio asked staffers to issue “stop-work orders” on nearly all “existing foreign assistance awards”, CNN reported.

The memo said the administration would be developing standards for a review of the assistance, to ensure it is “aligned with president Trump’s foreign policy agenda”.

“Decisions whether to continue, modify, or terminate programs will be made following this review,” the memo read, adding that it should be completed within 85 days. This review is meant to be sent to Mr Trump along with a recommendation from Mr Rubio on which foreign assistance programs to continue.

The US provides more foreign aid worldwide than any other country, allocating approximately $60bn for foreign aid in 2023.

The order’s lack of exemptions for life-saving health programs, such as clinics and immunisation initiatives, has caused concern and alarm among humanitarian organisations

“The stop-work order is completely reckless,” a senior official at USAID told NPR on condition of anonymity.

“The impact of this stop order is meant to negatively disrupt not just US foreign aid programs and the intended beneficiaries of these programs but the daily lives of people who deliver this critical aid: people with families to take care of, who have to buy food, pay rent and utilities. Yes, reform of US foreign aid is desperately needed but these draconian measures are unhelpful.”

Abby Maxman, head of Oxfam America, said: “By suspending foreign development assistance, the Trump administration is threatening the lives and futures of communities in crisis, and abandoning the United States’ long-held bipartisan approach to foreign assistance which supports people based on need, regardless of politics.”

“These are bilateral decisions but nonetheless we expect those nations who have the capability to generously fund development assistance,” said United Nations’ deputy spokesman Farhan Haq.

Some aid projects began receiving their first stop-work orders under the freeze on Friday afternoon.

Some organisations were also interpreting the directive as an immediate stop-work order for US-funded aid work globally, a former senior US Agency for International Development official, under the condition of anonymity, told The Associated Press. The official also added that many organisations might stop operations immediately to prevent incurring further costs.

The memo excludes all countries other than Egypt and Israel that receive foreign military funding from the US, such as Ukraine or Taiwan.