[13] In November 2021, Baker and several fellow University of Otago academics including Dr Lucy Telfar Barnard, Dr Jennifer Summers, and Lesley Gray criticised the Managed Isolation and Quarantine (MIQ) system's requirement that vaccinated travellers be tested as "inconsistent and arbitrary," asserting that they posed a lower risk of contracting COVID-19 than Aucklanders during the Delta variant.

[14] In December 2021, Baker expressed concerns that the Government's new COVID-19 Protection Framework ("traffic light system") in and abandonment of internal borders could lead to a rise in cases but added that the infection could be blunted by vaccination efforts and the warmer summer weather.

[15] In mid-December, Baker advocated that the Government delay its planned reopening of New Zealand's borders in January 2022 to counter the spread of the SARS-CoV-2 Omicron variant.

"[16] In early January 2022, Baker questioned the effectiveness of the "traffic light system" in dealing with Omicron community outbreaks and has advocated localised lockdowns.

[19] In mid-October 2022, Baker advocated the reinstatement of a form of the alert level system after the country reported its first case of the Omicron subvariant BQ.1.1 on 13 October.

[20] In early November 2022, Baker advocated reinstating mask requirements for public transportation and flights to combat rising COVID-19 hospitalisation and death rates caused by the third wave of COVID-19 sweeping through New Zealand in 2022.

[21] On 10 April 2023, Baker urged the New Zealand Government to retain the few remaining COVID-19 restrictions including the mandatory seven-day isolation period for positive cases and mask wearing at hospitals.

[22] In response to rising case numbers, hospitalisations and deaths reported on 17 April, Baker stated that New Zealand was experiencing its fourth wave of COVID-19 infections.

Baker advocated encouraging people to get the new Covid vaccine booster, isolate if they are infected, and wear facemasks in poorly ventilated environments.

[28] In 2022, he was awarded the Callaghan Medal by the Royal Society Te Apārangi for "science-informed commentary on the Covid-19 pandemic and other major public health issues in Aotearoa New Zealand".