NPOs are traditional places for CIA agents.

Tends to make them targets of suspicion.

Source: My father[0] was in the CIA, and worked at an NPO, in Africa.

[0] https://cmarshall.com/miscellaneous/MikeMarshall.htm

If nothing else, the "Political Operations Abroad" section of USAID's wiki has some links and background.

Source for Top Secret info? No, but I'm reminded of https://en.wikipedia.org/wiki/CIA_fake_vaccination_campaign_... (not USAID, a different organization)

If you don't mind listening to right-wing adjacent commentators, Mike Benz document those links extensively on his podcast. For exemple:

https://www.youtube.com/watch?v=yR09YYX-3fg