Guatemala City, Guatemala - Secretary of State Marco Rubio said Wednesday the US would keep funding international aid projects after a "bottom-up" review, as most staff at the country's massive humanitarian agency are set to be placed on leave.

Rubio, on a visit to Guatemala, insisted that President Donald Trump's administration only reluctantly issued sweeping orders that included bringing back almost all overseas staff of the US Agency for International Development (USAID).

"We are now going to have to work from the bottom up, instead of the top-down, to identify which programs should be specially designated and therefore exempted," Rubio told reporters.

Rubio repeated his claim that USAID had been unresponsive to requests by the Trump administration to review its funding.

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"Our preference would have been to do this in a more orderly fashion from the top down, but we had no cooperation," Rubio said.

"We had individuals, even after the orders were issued, that were still trying to push payments in contravention and direct insubordination," he said.

"So now we've had to do it in the opposite direction. It is not the direction I wanted," he said.

Rubio said that all future projects would be assessed on whether they "make us safer, stronger and more prosperous" and whether they "align with the foreign policy" under Trump.

"This is not a charity. These are not private funds. This is American taxpayer funds. We have an obligation to spend it wisely," Rubio said.

Elon Musk, the billionaire tech entrepreneur leading the Trump administration's cost-cutting efforts, has used much harsher language on USAID and vowed to destroy it.

Rubio was made acting director of USAID, which is putting virtually all of its staff on administrative leave starting Friday.