Humza Yousaf said there was no way to “sugarcoat” the situation as the perfect storm puts intensive pressure on the health service from a number of fronts.
Speaking on Good Morning Scotland, Mr Yousad said: “You have the pandemic backlog that has built up over the last 21-odd months.
“We have high levels of staff absence, again much of that increasing because of its higher transmissibility.
“Then of course we are also treating a number of people who are in hospital with Covid-19.
“So those pressures, coming during the winter months when we tend to see busy hospitals busier, will put more pressure on our health service… this is going to be an extremely challenging period.”
He said that the Scottish Government will do everything it can to support the health service, including trying to support more Covid-19 patients being treated at home who previously would have been admitted to hospital.
He said they would offer support and treat these people with antivirals, and hopes this step will help with the capacity challenges facing the NHS.
Mr Yousaf reiterated the First Minister’s message from Wednesday that we are entering a new phase in the pandemic.
“We’re almost two years into this pandemic,” he said.
"We have to look at how we control that [the virus] in a more sustainable way because we understand the long term harms that Covid-19 has on not just people’s health, but on the economy and on people’s mental health, as well as many other aspects of society too.”
While he didn’t rule out lockdowns, the health secretary said he hopes to never see another one again given how damaging they are to Scottish society.
“There are certainly no plans for any lockdowns,” he said.
“What I would say though is when we talk about adapting in a more sustainable way to controlling the virus, that doesn't mean throwing caution to the wind, that's really important to signal.
"But I don’t envisage any lockdowns in the immediate future certainly.”