Welsh NHS charities with links to Africa have said some people they invite to Wales are being humiliated by the way the Home Office handles their visitor visa applications.
Experts with advice for the health service are among those who have had applications refused, they said.
The Welsh Government launched the Wales For Africa programme in 2006.
The Home Office said all UK visa applications were considered on their individual merits.
It added this was in line with UK immigration rules and guidance.
Pontypridd GP Geoff Lloyd said while more than 100 Ugandans have visited the town over the last 10 years through the charity Pont, some were now being refused entry.
He said: "Most problematic of all, is that we started finding that the vast majority of visas were being denied and they were being denied at the last moment, which turned our plans to bring visitors of Uganda over into total chaos and left a lot of very frustrated people both in Wales and Uganda."
Duncan Cameron, a recently retired consultant paediatrician at Glan Clwyd Hospital in Denbighshire, said it had charitable links with a hospital in Ethiopia and last year it invited two senior clinicians to visit.
But he said their visas were turned down because the Border Agency was not sufficiently reassured the Africans would return home.
Former First Minister Rhodri Morgan, who died in May, set up the Wales for Africa programme.
His wife, Labour AM Julie Morgan, said Wales learnt a lot from the projects and vice versa, and called the problems "deeply disturbing".
"Some of the visitors who have come here have been treated very badly at the borders, like dirt really," she said.
"They have been suspected of coming here to stay. These highly qualified professional people who have so much to give to our health service, they are suspected of coming to Wales and wanting to stay.
"They are treated as though they are trying to get something out of our country rather than give something."
Dr Tony Jewell, Wales's former chief medical officer, told a Wales for Africa conference in Cardiff he had taken the matter up with MPs.
He said: "I think people do recognise this is a problem, and sometimes this is hard to understand.
"These are either deans of medical schools in Africa or leading politicians in their own country and they'll come to give a talk and they'll go back. They aren't subversive economic migrants."
Dr Grace Kodindo, a consultant obstetrician in Chad, was refused a visa but the Home Office reversed that decision after the Cardiff West MP Kevin Brennan raised the matter in parliament.
She was, however, kept waiting at Heathrow Airport for several hours before being let through.
"I felt like I was nobody. A criminal. A no-good person. I was not expecting at all this treatment, especially as in 2007 I was invited to the House of Commons. I gave a talk there. So that was not my first time," she said.
Dr Kodindo was invited to Wales by Angela Gorman, a paediatric nurse in Cardiff who had seen a BBC Panorama programme about her work.
It inspired Ms Gorman to found the charity Life for African Mothers and she said she believes the difficulties with visas are undermining charities' work.
"It's just this frustration and anger at this attitude that everyone who comes to the UK wants to stay here and that's not the case," she said.
The Welsh Government said health secretary Vaughan Gething has written to the Home Office to make representations on behalf of those wanting to come to the UK as part of the Wales for Africa programme.