Face coverings have been recommended since the return to school in March - but that will end as part of the phasing out of lockdown measures.
There have been concerns that masks obstruct communicating and learning.
But education and health leaders in the region warned the decision to remove masks was a “step to soon” with the evidence on safety and lack of covid vaccination roll out for students and staff.
Samantha Twiselton, deputy for the Doncaster opportunity area, one of three Yorkshire opportunity areas, alongside Bradford and the North Yorkshire coast, highlighted the use of masks for secondary school children was particularly important across the region.
She said in some places infection rates “remain relatively high” and there were added risk factors such as several generations living in the same household.
She said: “While there are clearly arguments both ways, protecting the health of school staff and pupils must be the primary consideration.”
Meanwhile a health leader in Bradford has warned people need to remain vigilant across Yorkshire due to the high number of Covid-19 cases.
Professor Mahendra Patel who since the start of the pandemic has led outreach work to highlight important health messages to BAME communities in Yorkshire and beyond, in languages other than English, said: “I think this is too early to take this step because as we know schools are an incredible vehicle for transmitting the virus really.
“I would want to be more cautious before we take this step because as we know schools are an incredible vehicle for transmitting the virus really."
While expressing his “delight” on the number of Covid-19 vaccinations rolled out across the UK so far Professor Patel warned the public must not “drop its guard” against the deadly virus. He highlighted the "ongoing danger" posed by new Covid variants that have entered the country.
Prof Patel said: "We are not out of the woods. We have variants - some of the deadliest, really powerful and potent variants that we are still seeing - India, Brazil, Africa.
"Add to this the younger population are not yet vaccinated fully and they are the more mobile people."
He added: “Those younger groups of people could be the source of transmitting the more resistant strains that we keep talking about.
“We are still exposed until we have largely everyone vaccinated - and we are a little bit away from that.”
Paul Whiteman, the general secretary of the school leaders’ union NAHT, said: “Parents, pupils and staff will want to understand why removing the requirement for face coverings in classrooms is considered appropriate when it is not for other enclosed spaces.
“No one wants to see pupils or staff wearing face masks for longer than is necessary. But the government should not rush into changing this policy without careful consideration of all the scientific evidence surrounding the wearing of face coverings in schools.
"Clearly, the safety and wellbeing of all members of school communities and their families should remain our primary concern."
England's Education Secretary Gavin Williamson said the latest steps meant people would be able to mix indoors again - and "in line with the latest data, we no longer need to recommend that face coverings are worn in the classroom.
"Over the past year we have always put the wellbeing of pupils and staff first, and this step is now the right one," said Mr Williamson.
John Simpson of Public Health England, added: "It's important to strike a balance between Covid-19 protection and student well-being" and that "scientific studies show that Covid-19 transmission in schools remains low".
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