The move from Bayfordbury to Norwich, first proposed in 1962, agreed by the council in June 1965 and achieved in 1967, aroused dismay and protest from past and present staff members, scientists in the genetical and biological fields and others. The protest movement came to a head in 1965-1966. Darlington played a prominent part, writing letters to the national and specialist press, mobilising support from colleagues, learned societies such as the Genetical Society and the Royal Society, and from the Member of Parliament for Maidstone, John Wells. Questions were asked in the House of Commons, and the role of the Charity Commissioners was challenged.

The move envisaged the transfer of the Departments of Cell Biology and Genetics, with professorial status for their heads, to the School of Biological Sciences of the University of East Anglia. Other existing departments were to be closed, and practical horticultural and agricultural work would be carried out at a separate field station. Thus, the university connection which had once existed with London would be re-established at East Anglia, but at the cost of the truncation of the Institute's departments, the separation of fundamental and practical research, and the end of the John Innes as an independent integrated establishment. Terms such as 'dismemberment', 'dissolution' and 'dispersal' are often used (and not only by Darlington) in the papers on the subject.

Darlington himself saw the proposed action of the Trustees as a further manifestation of the divided responsibilities, multiple authorities and unworkable constitution of the Institute with which he had wrestled from 1936 onwards (MS. Darlington c. 10/B.19-B.21). His own contributions to the debate reflect this extra dimension as well as seconding the criticisms of others, and often refer to the memoranda he submitted in 1953 (MS. Darlington c. 11/B.48) and 1955-1956 (MS. Darlington c. 12/B.52-54).