While NHS Blood and Transplant manages organ donations and supports transplant centres, services are commissioned and paid for by NHS England.
But in a letter to NHS England and a small group of patient advocates, Manas said the central body had created a “fragmented” system “with poor accountability”.
There is a “mismatch”, he said, between each hospital’s waiting lists, organ availability, capacity to carry out surgeries and the availability of operating theatres.
This is “leading to last-minute cancellations [and] unpredictable utilisation of donated organs,” he warned.
The reported in March that the UK, once a world leader, had fallen behind major Western nations in heart and lung transplantation, though it fares better in other areas such as kidney transplantation.
The NHS transplants one in 10 lungs and one in seven hearts that are donated – half the proportions seen in some other countries.
It has not invested in modern technology at the same rate as other countries, and suffers from a lack of theatre space, intensive care beds and staff.
Wales and Northern Ireland do not have a heart and lung transplant centre, so patients commonly travel to England for surgery. There is one heart transplant centre in Scotland.