The Regional Initiative in Science and Education (Rise) seeks to address the chronic lack of qualified lecturers in sub-Saharan universities. Staff running the project said that almost all the graduate students in the region had to be supported by external organisations because of the lack of funding from national governments.
Arlen Hastings, executive director of the Science Initiative Group, which runs Rise, said that African universities do not have enough qualified tutors and had "crowded classrooms with teachers maybe one year out of school".
The SIG is an international group that tries to foster science in developing countries. Since Rise began in 2008, about 100 scholars have been given funds to pursue science or engineering postgraduate qualifications in nine African countries.
Alan Anderson, a research and editorial consultant at SIG, said that the initiative targets students who aim to be academics but who are "stuck professionally". He said it grew out of a meeting of African vice-chancellors in 2008 who had "expressed a consensus that they needed more better-trained faculty".
However, while the initiative aimed to stem the brain drain from Africa, there were no contracts tying those who were funded to working in the continent. Instead, Rise scholars stayed because they work on solving problems related to where they live, he added.
Ms Hastings said that Rise could make a "tiny, tiny" difference, but the lack of trained faculty in Africa was a problem that would get worse before it got better.
The programme has received more than $10 million (£6.4 million) from the Carnegie Corporation of New York, funding it until 2016, and Ms Hastings said it was now in discussions with the World Bank and African governments for additional income so that it could increase its operations tenfold.
She said Rise was also looking to expand into francophone African countries and possibly North Africa.