Video report by ITV News Political Correspondent Daniel Hewitt
The PM has so far been resisting pressure to adopt advice from the World Health Organization that all children aged 12 and over should wear coverings when social distancing is more difficult.
Labour says Mr Johnson "must listen" to a "growing body of evidence" which suggests use of face coverings in communal areas in secondary schools helps protect students and staff from coronavirus.
Earlier the PM told reporters he would "look at the the changing medical evidence as we go on".
“If we need to change the advice then of course we will," he added.
Scotland has not only adopted the WHO guidance on face coverings for secondary school pupils, but has gone further by asking all children aged five and over to wear them on school buses.
Labour's Shadow Education Secretary Kate Green said: "The prime minister must listen to this evidence and act quickly to give certainty to parents and teachers who are just days away from schools reopening.
"The last thing concerned parents and pupils need is another last minute u-turn from this government that throws school plans into chaos."
Asked why he was ignoring World Health Organisation advice that children aged over 12 should wear masks, Prime Minister Johnson said: “The overwhelming priority is to get all pupils into school.
“And I think that the schools, the teachers, they’ve all done a fantastic job of getting ready and the risk to children’s health, the risk to children’s wellbeing from not being in school is far greater than the risk from Covid.
“If there are things we have to do to vary the advice on medical grounds, we will, of course, do that.
“But as the chief medical officer, all our scientific advisers, have said, schools are safe.”
On Monday, a Number 10 spokesperson said the government is “conscious of the fact" that face coverings "would obstruct communication between teachers and pupils".
The mayor of London is considering whether to defy the government by advising face coverings for teenagers at schools in the capital.
Sadiq Khan said it is "important that lessons are learned" from other countries which have already reopened their schools.
Nicola Sturgeon changed advice in Scotland after an outbreak at a Dundee school saw 19 staff members and pupils infected with coronavirus.
Mr Khan said: “It is vital that we do all we can to ensure we limit the spread of coronavirus in all settings, including in schools.
“The World Health Organisation has advised children over 12 to wear a face covering where they can’t socially distance, and as more countries are introducing them in school corridors and communal areas, it’s important that lessons are learned.
“I have continually called on Government to respond to the latest health advice and my team are speaking with officials in Scotland to ensure we have the most up-to-date advice ahead of our schools returning.”
The wearing of masks could apply to corridors and communal areas, but may not be as necessary in classrooms where it is easier to socially distance.
Oasis Academy, a chain of 52 schools across the country, has taken matters into its own hands, with its founder ordering all staff and pupils to wear face coverings when they return in September.
Steve Chalke told the BBC face coverings will be considered part of the uniform adding that “we will consult with everyone but this is the way we are going.”
He said the move has been made because “we believe this makes our schools safer than they would otherwise be”, not just for students and staff but also their families.
Mr Chalke, who said it is “all about common sense and taking responsibility”, told the BBC: “There is no such thing as being Covid-safe, just Covid-safer.
“Based on our values and our sense of morality – these are the moves that we are choosing to make.”