Penicillin patents became a matter of concern and conflict. Chain had wanted to apply for a patent but Florey had objected, arguing that penicillin should benefit all. Florey sought the advice of Sir Henry Dale, the chairman of the Wellcome Trust and a member of the Scientific Advisory Panel to the British Cabinet, and John William Trevan, the director of the Wellcome Trust Research Laboratory. On 26 and 27 March 1941, Dale and Trevan met at Oxford Universitys Sir William Dunn School of Pathology to discuss the issue. Dale advised that patenting penicillin would be unethical. Undeterred, Chain approached Sir Edward Mellanby, then Secretary of the Medical Research Council, who also objected on ethical grounds. As Chain later admitted, he had "many bitter fights" with Mellanby, but Mellanbys decision was accepted as final.
In 1945, Moyer patented the methods for production and isolation of penicillin. He could not obtain patents in the US as an employee of the NRRL, but filed for patents with the British Patent Office. He gave the license to a US company, Commercial Solvents Corporation. When Fleming learnt of the American patents on penicillin production, he was incensed and commented:
The patenting of penicillin-related technologies by US companies gave rise to a myth in the UK that British scientists had done the work but American ones garnered the rewards. When the Rockefeller Foundation published its annual report in 1944, The Evening News contrasted the foundations generous support of the Oxford teams work with that of the parsimonious MRC. In April 1945, the British firm Glaxo signed agreements with Squibb and Merck under which it paid 5 per cent royalties on its sales of penicillin for five years in return for the use of their deep submergence fermentation techniques. Glaxo paid almost £500,000 () in royalties between 1946 and 1956. The controversy over patents led to the establishment of the UK National Research Development Corporation (NRDC) in June 1948. This organisation collected government patents and charged royalties on them.