Mr Swinney said the nature of the virus, combined with variants, would mean that protection from emergency coronavirus legislation would still be necessary in three months.
In a ministerial statement to Holyrood on the Coronavirus Acts, Mr Swinney gave a report ahead of a vote to extend emergency powers granted to the government. Currently, emergency powers expire on September 30.
In response to a question on Wednesday from Scottish Conservatives’ Donald Cameron as to whether it was necessary to extend the legislation beyond its existing limit, Mr Swinney said: “We have got to go about making sure we have in place appropriate arrangements that enable our public services – and a wide variety of other examples to be able to be conducted within a context that is compatible with the current public health environment in Scotland.
"So this question that Mr Cameron raises is one which needs to be addressed by considering the public health emergency that I expect us still to be facing in September.
"And because of the nature of coronavirus, the mutations of the variants that we are all facing and having to respond to, on that basis, the necessity of these provisions being in place is apparent to me.”
Mr Swinney pointed to Wednesday’s case figures, with more than 1,000 cases of Covid recorded in Scotland.
He said: "The number of cases for example, today, was over 1,000 and that is an example of the development of the new variants, so we have to make sure that we have a legislative framework in place that adequately addresses the public health emergencies that we face.”
The Deputy First Minister said that 99 per cent of people in Scotland aged 50 and over – 2,162,865 people - have now received at least their first dose of the vaccine. But he said emergency provisions would still be necessary in the autumn, when not all adults would have received a second jag.
Mr Swinney said: “We are in a situation where we still don't have absolute clarity that we can extend the vaccination programme to children.
"It is looking encouraging, but we don't have absolute clarity and authorisation to do so. So many individuals over the age of 18, at the very least, will still be requiring the second dose of their vaccination and they won’t get that until later on in the year.
"These provisions are not new provisions that have been introduced. [They are] simply an extension of certain provisions to ensure we have the capacity and the capability to manage the public health emergency.”
Scottish Conservative MSP Murdo Fraser said the extension should be delayed until September, when the existing emergency powers were due to expire, rather than be “rushed through” in the two weeks before parliamentary recess.
Mr Swinney said: “There are some extraordinary arrangements which don't actually give ministers lots more powers, but give various organisations that exercise functions, such as our courts for example, to be able to operate on a different model.
"I would suggest the courts, and other organisations, would require more notice than if we were to handle this legislation at the start of September.”