Steve Barclay said the Government had developed a "better understanding" of the virus over the past two years and was "in position" to target vaccinations at those most at risk.
And in a personal appeal to readers he urged as many people as possible to take up a booster jab ahead of potentially rising cases from next month.
Mr Barclay has warned the NHS faces a triple threat from flu, Covid-19 and the cost of living crisis – all of which are expected to increase demand and put strain on services.
He told the Star: "We know the risk of Covid spreading is higher in winter than in summer. That is why we're taking the steps we have, not only with Covid, but also to expand the cohort for the flu jab.
"We're doing the same with the Covid jabs, and we've also had the benefit of developing a better understanding about Covid than we did when it first hit us.
"It means so we're able to ensure – with the benefit of that insight we have picked up – that we are in position to target those who are most at risk.
"We've prepared the roll-out and I'd urge all readers to take up their booster. It really is essential that people do so."
Under plans to increase protection against viruses, everyone aged 50 and over will be among those offered a Covid booster and a flu jab this autumn.
Mr Barclay said the NHS was in a "real sprint" to get ready for September and that decisions over issues such as the hiring of staff could not wait until after a new PM was elected.
According to the latest figures Covid infections are continuing to fall in the UK, with infections dropping by 500,000 to 2.6million in the week ending July 26.
However, the World Health Organisation has warned of a "challenging" autumn ahead, with cases in some parts of Europe already on the rise.