Parents have lashed out at John Swinney after he announced secondary pupils as young as 15 are to be forced to wear face masks in class across most of Scotland from Monday.
The Education Secretary published guidance ordering children in the fourth, fifth and sixth years of secondary school and their teachers to start wearing face coverings in classrooms.
They should also wear masks in school corridors when they are moving around and in communal areas.
In addition, the guidance said face coverings should be worn by adults in all Scotland's schools where they cannot remain two metres apart from staff or pupils.
Mothers and fathers were ordered to wear a mask from Monday when they drop off or pick up their offspring.
But a high-profile parent's group reacted furiously to the change for older pupils, arguing that wearing a face covering for several hours was "incredibly uncomfortable" and would hinder their education.
UsForThem Scotland, which earlier this year helped force Mr Swinney into a U-turn to keep schools open, questioned the evidence on which the change had been based and said it appeared to have "been made on a whim."
The National Deaf Children's Society warned it would present "serious challenges" to deaf pupils.
A report by an expert advisory group to the Scottish Government recommended parents and adults wear face coverings on secondary school sites but did not mention pupils.
However, Mr Swinney said the evidence suggests "there is slightly higher infection and transmission risks for people around the age of 16 to 17."
The rules apply to state schools in 19 of Scotland's 32 local authority areas, which Nicola Sturgeon has placed in level 3 of her five-tier lockdown system.
They include most of the Central Belt such as Glasgow and Edinburgh, Lanarkshire, Ayrshire, Dundee and Stirling.
The restrictions also apply to level 4, the highest tier that imposes almost full lockdown, but no councils have yet been placed in that. Ms Sturgeon's tiers are numbered zero to four.
The Scottish Government published the latest advice from its Covid-19 advisory sub-group on education, which found there has been a low level of Covid-19 transmission in schools since they reopened in August.
But it warned this could increase thanks to the surge in cases in the general population. It said case numbers were higher for older children, before "dropping off sharply" for youngsters aged 15 and under.
Given the recent surge in cases, it recommended the advice on face coverings be "strengthened and augmented to manage the main area of risk within schools, which is adult to adult transmission."
Among the group's recommendations for secondaries was that parents, classroom assistants and teachers should generally wear masks, and the latter should do so even when not in class. However, it did not recommend pupils do so.
Mr Swinney insisted ordering pupils to wear masks in class reflected said "updated scientific and health advice". He said: "Keeping schools open remains our priority but that can only be the case if schools are safe."
The Education Secretary added: "We constantly review the guidance on school openings along with our local authority partners, trade unions, parental representatives and other stakeholders to ensure we are taking all the necessary measures to ensure our schools are safe."
He also unveiled updated guidance for teachers and pupils who are at risk thanks to their health conditions, saying parents in level 3 areas should consult their GP over whether it was safe for their children to attend.
But Jo Bisset, organiser for UsForThem Scotland, said: "Parents suspect this decision has been made on a whim, and is merely just the start of an escalation which will eventually see all pupils forced to wear masks.
“It will be incredibly uncomfortable for young people to spend several hours a day in a mask, and could impact on their learning and education." She also expressed concern about the impact on vulnerable pupils and those with autism or hearing difficulties.
Alasdair O’Hara, head of policy for Scotland at the National Deaf Children’s Society, said: "The safety of pupils and staff is the number one priority, but using face masks and coverings in classrooms will present serious challenges for deaf children.
“Unless their needs are considered at every stage, deaf children’s education, life chances and mental wellbeing will be on the line.”
Jamie Green, the Scottish Tories' Shadow Education Secretary, said: "Once again, significant Covid-19 restrictions are announced by the SNP government hours after parliament closes. Had they made this known on Thursday, this could have been properly debated.
"Parents across Scotland understood the guidance around staff wearing masks in schools, and older pupils wearing them in public areas, but the SNP has not explained why this latest move is necessary."
The Educational Institute of Scotland, the country's largest teaching union, said the change was "a reflection of the greater risk posed by higher levels of community infection."
But Larry Flanagan, the union's general secretary, said: "We remain dissatisfied with the lack of specification on social distancing between pupils, which is exhorted but remains impossible to achieve in full classrooms.”