President Donald Trump's decision to freeze foreign assistance has sent aid staff in Africa into "panic mode", with even HIV experimental treatment programmes stopped dead in their tracks.

Trump last week ordered a suspension of foreign assistance, while his billionaire ally Elon Musk has boasted he is putting the vast US humanitarian agency USAID "through the woodchipper".

That has included a 90-day suspension of all work by the President's Emergency Plan for AIDS Relief (PEPFAR), which alone supports more than 20 million HIV patients and 270,000 health workers, according to an analysis from the Foundation for AIDS Research (amfAR).

Among its programmes, PEPFAR currently provides anti-retroviral treatments to 679,936 pregnant women living with HIV both for their own health and to prevent transmission to their children, the analysis said.

"During a 90-day stoppage, we estimate that this would mean 135,987 babies acquiring HIV," it said.

US Secretary of State Marco Rubio, who has been named acting head of USAID, has said "life-saving treatments" would be exempt from the freeze.

But frontline workers in Africa say facilities have already shut down.

"As we speak nothing is going on," said Aghan Daniel, head of a USAID-funded team of Kenyan science journalists providing information on health issues.

He told AFP research projects had abruptly stopped, even for patients midway through experimental treatment programmes.

He highlighted the MOSAIC (Maximizing Options to Advance Informed Choice for HIV Prevention) project, funded under PEPFAR, which tests new drugs and vaccines.

"The people who were the study candidates are going to have adverse health results because the study has just stopped all of a sudden," Daniel told AFP.

His own team of six science journalists have all lost their jobs, too.

"A lot of people are going to die because of lack of knowledge," he said. "One of the key approaches to bringing down HIV numbers in Africa is through provision of information. This includes raising awareness about sex, as well as treatments like lenacapavir (an antiretroviral), pre- and post-exposure prophylaxis and other drugs."

- 'Life and death' -

Founded in 1961, USAID has an annual budget of more than $40 billion, used to support development, health and humanitarian programmes around the world, especially in poor countries.

It is not just HIV programmes that have shuttered.

A staff member of a USAID-funded programme in Kenya said Trump's decision had landed "like a bombshell", throwing people "into panic mode".

"We will have more people succumbing to these diseases like tuberculosis, cholera," the source said.

The charity itself is now unable to pay rent or salaries, with employees put on compulsory unpaid leave.

At a USAID office in Addis Ababa, Ethiopia, AFP saw people clearing out their desks on Wednesday.

Despite Rubio's waiver, "a lot of uncertainty remains," said a staff member at an NGO working on food security in conflict zones, who asked to remain anonymous.

"What constitutes life-saving work? Are vaccines life-saving, or nutrition programmes for the severely malnourished?" he said.

"Stopping some of these programmes even for a few days could make the difference between life and death for some of the people we serve," he said.

Like others, Daniel said the impact could have been tempered with adequate notice.

"We have too many emergencies in the world -– we didn't need to add another one," he said.