Under the new guidance, all staff, visitors and pupils in Year 7 - the first year of secondary school - or above, are "strongly advised" to wear a covering, unless exempt.
The measure covers all education establishments including universities, as well as childcare settings such as early years care.
The guidance does not mean masks should be worn in classrooms but it is advised that they are worn in communal areas like corridors.
But Richard Sheriff, chief executive of Red Kite Learning Trust, which runs a number of schools in Leeds and also member of the Association of School and College Leaders, urged the Government to use stronger wording and offer more support to headteachers.
Questioning why wearing masks in schools was merely "recommended", unlike the compulsory rule in public spaces such as shops, he said: "I don't think what's been announced is terribly helpful," adding: "It leaves school leaders feeling exposed once again".
He urged the Government to make a "mandate from above" so headteachers can enforce mask-wearing, adding: "As school leaders we take the virus and its impact extremely seriously and want to do all we can to control it in our schools and beyond our schools."
His views were echoed by Terry Bambrook, a health and safety officer and case worker for the Leeds branch of the National Education Union (NEU).
He said the working is not helpful for headteachers and “couldn’t understand” why the Government had not made them mandatory, as they had in shops and public transport.
“[Headteachers] are in a hell of a position really. Guidance from the DfE doesn’t always come out in a timely fashion so there is not time to react to it. We have an awful lot of respect for the school leaders and seek to work with them, in schools and colleges, to try and get the best protection for everybody - for the kids as well as staff and their families and in turn the community beyond.”
Terry said Covid-19 rates in Leeds had been decreasing for the age groups five to nine and 10-14 up to and during the recent half term break but these were now increasing again.
“And masks would help and would slow it down,” he said. “It’s as simple as that.”
Current case rates for the city stand at 638 per 100,000 for the five to nine-year-olds, as of November 24, compared to 521 per 100,000 on November 9.
The rolling rate for those aged 10-14 was 729.4 as of November 24, up from 534 on November 9.
Nationally, the number of children out of school for Covid-related reasons in England has risen over the past fortnight, figures show.
The Department for Education (DfE) estimates that 2.6 per cent of all pupils - more than 208,000 children - were not in class for reasons connected to coronavirus on November 25.
This was up from more than 130,000 children, or 1.6 per cent of all pupils, on November 11.
Given details of the new controls, Education Secretary Nadhim Zahawi said: "The news of a new variant - the so-called Omicron variant - will have understandably caused concern for people across our country, including our teachers, wider education and childcare staff, parents, pupils and students.
"We are already taking targeted and proportionate action as a precaution while we find out more information about the new variant.
"As we do so, we will continue to prioritise children's and young people's education and wellbeing, making sure education and childcare settings are as safe as possible and children continue to benefit from classroom teaching.
"We are working with education and childcare settings to enhance safety measures where needed, including introducing isolation for 10 days for close contacts of suspected Omicron cases.
"I'd like to thank everyone working to support our children and young people for their patience and hard work."
The guidance is temporary and will be reviewed in three weeks, the Department for Education said.
Students in Year 7 or above should also continue to wear face coverings on public and dedicated school transport, unless they are exempt, the DfE said, and staff and students should continue to be encouraged to test themselves twice a week using lateral flow tests.
The department also said schools, out of school settings and colleges will "want to consider" whether to go ahead with any planned international trips at the current time, given the potential risk to education from the need to isolate and test when returning to the UK.
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