Naki became one of four technicians in the research laboratory at the medical school. He assisted numerous young surgeons who spent time training in the animal laboratory to perform research—then transplantation of kidneys, hearts, and livers—and to obtain higher research degrees. Despite being listed in hospital records as a cleaner or gardener, he was paid the salary of a senior lab technician, the highest pay the hospital could give to someone without a diploma.
Naki is best known for being incorrectly cited as a surgical assistant to the world's first heart transplant, most famously by the Economist magazine , who subsequently retracted the story . The story, which proved to be a myth, said that when Barnard returned from the United States to develop cardiac transplant techniques, Naki was enlisted as his assistant, where he assisted in the removal and cleaning of Denise Darvall's heart, who was fatally injured in a car accident, during a marathon surgical operation on 3 December 1967. However, surgeons at Groote Schuur, the hospital where the transplant was performed, refuted this claim as did some sources close to Naki.
The process was assisted by hints from Barnard that Mr Naki had helped him in ways that were not fully known, and by the fact that, under apartheid, any such help on white human subjects would have had to be secret anyway. In the end, a story took shape that looked so plausible to the outside world that many famous publications, including the Lancet, the British Medical Journal, the Economist and many others accepted it. Yet the same story appeared so ridiculous to the University of Cape Town, staff say, that they did not trouble to deny it.
Naki did however help assist a number of the surgeons involved in the operation in their earlier medical training and in 2003, the university awarded him the degree MMed [honoris causa], stating, "Mr Naki assisted with the experimental work that preceded...the historic first heart transplant."
Despite his lack of formal training, Naki provided valuable training to thousands of student surgeons without receiving any formal acknowledgement. Barnard would later praise Naki for his role as a teacher and for his skills as a "surgeon". Barnard himself admitted before he died that "He (Naki) probably had more technical skill than I had". Indeed, he used this skill to become a trainer of over 3000 future surgeons, renowned for expecting high standards from his students. Meanwhile he would use his lunch breaks to read the Bible to the homeless people gathered in the local cemetery, and warn them against alcohol and cannabis.