John Swinney has defended the decision to keep schools open in areas which are being moved to the toughest level of lockdown restrictions.
It comes as the EIS, Scotland's largest teachers' union has said that school closures should not be ruled out and that blended or part-time learning should be in the mix.
The deputy first minister said keeping schools open was "absolutely central" to the wellbeing of children and young people.
It comes as more than two million people are to be placed in level four of Covid restrictions from Friday.
Non-essential shops, pubs and restaurants will be forced to close in 11 areas across central Scotland.
It comes as the number of pupils off school for coronavirus-related reasons has soared in Glasgow.
Nearly 5000 youngsters had an absence linked to Covid-19 in the most recent figures – the highest since the Scottish Government started tracking daily levels in August.
According to the Scottish Government over 0.2% of pupils tested positive for coronavirus in the first nine weeks of the school term restarting in Scotland.
Nicola Sturgeon said the findings reinforced her view the benefits of reopening schools outweigh the risks of increasing transmission rates.
Public Health Scotland found 1,621 positive cases were linked to schoolchildren, with 1,021 of those in secondary schools.
More than three-quarters of schools did not have any recorded cases during the time period, it said.
Mr Swinney insisted public healthcare evidence showed schools were "not contributing significantly" to increased cases.
Discussing the report at the coronavirus briefing in Edinburgh on Wednesday, the First Minister said cases in schools tended to reflect rates of transmission in the wider community.
She said: "While we will continue to listen carefully to all concerns, these findings do reinforce our view that at this time, the benefits young people gain from being in school outweigh the overall impact of schools on transmission rates.''
Ms Sturgeon said she did not "dismiss'' the concerns of teaching unions but added: "Out of 700,000 school pupils, 1,600 cases were positive.
"That's not no cases, and I'm not saying there's zero risk of transmission, but it puts it into some kind of context and perspective.''
The First Minister said there is a responsibility on councils to make sure children receive "the educational provision they need" if they have to self-isolate.
She added the use of lateral flow coronavirus tests, which provide results much faster than existing PCR tests, is being considered for use in schools.
This will depend on medical regulators approving lateral flow tests for use without medical supervision, she said.
A separate paper on the transmission of the coronavirus in schools reveals that, in the first term back after summer, over three-quarters of Scottish schools had no pupils who tested positive for the virus.
It also states that pupil Covid-19 related absence hit its highest level earlier this month; that in 305 schools (roughly 12 per cent of all schools) more than one pupil had tested positive in the first term back; and that almost a quarter of secondary schools had more than one case occurring in the same week, on at least one occasion.
In the last week of the first term of 2020-21, the paper says, six per cent of secondary schools had more than one pupil who tested positive in the same week, although the cases were not necessarily linked.
The level four rules will see the closure of non-essential shops, pubs, restaurants and gyms.
They will be imposed in East Dunbartonshire, East Renfrewshire, Glasgow, Renfrewshire and West Dunbartonshire.
North and South Lanarkshire, East and South Ayrshire, Stirling and West Lothian will also move to level four.
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