On 24 February 1965, McNicoll was promoted vice admiral and made Chief of Naval Staff (CNS) in succession to Vice Admiral Sir Hastings Harrington. By virtue of this position, McNicoll was head of the Naval Board and the functional commander of the RAN. McNicoll's term as CNS was characterised by a period of heightened activity for the RAN in light of the Australian commitments to the Indonesia–Malaysia "Konfrontasi" and the Vietnam War. He furthermore had to oversee an extensive modernisation of the fleet, with the introduction into service of the "Perth"-class destroyers, "Attack"-class patrol boats, and the initial batch of "Oberon"-class submarines. The Fleet Air Arm was also re-equipped with American fixed wing aircraft. Despite these acquisitions, the RAN possessed a rather thin and limited fleet during this period, which McNicoll blamed on past naval planning. He criticised the lack of foresight in earlier decisions that had led to "inconsistencies and inadequate estimating" in the future needs of the RAN, which had consequently left the fleet outdated and minimal. In addition to the RAN's materiel issues, McNicoll faced significant problems with morale and recruitment. A series of mishaps and accidents over the previous decade led to what naval historian Tom Frame termed as "an appreciable erosion of public confidence in the navy's professional standards". The situation intensified following the February 1964 collision between HMAS "Melbourne" and "Voyager". The two subsequent Royal Commissions into the incident subjected the RAN to unprecedented scrutiny and damaged the public perception of its senior leadership. McNicoll had to cope with the turmoil occasioned by these events and concerned himself with the restoration of morale in the Navy.