Speaking at a conference organised by her union and the Refugee Council, Chris Keates told delegates that free schools and academies could create "apartheid in our schools".
"The hallmark of a comprehensive system of education is that it is inclusive and provides equal rights and entitlements for all children and young people and for the workforce in schools," she said.
Keates added that government plans to cap immigration could also undermine the quality of educational provision.
"The UK benefits massively from the contribution of migrant workers in all sectors of the economy who make a major economic contribution and provide the services on which we all depend," she explained.
"Limiting the number of workers from overseas entering the UK also threatens to undermine educational standards, particularly in shortage subject areas. We cannot afford to close the doors on skilled overseas trained teachers if we are to secure the UK’s economic recovery."
Jonathan Ellis, director of policy and development at the Refugee Council, argued that refugee children and qualified refugee teachers too often face barriers to engaging with the UK education system.
"Working together with government, schools and training providers, it must be made easier for refugees who qualified as teachers in other countries to teach here so that we can make the most of a huge pool of talent, especially in subjects where teachers are in demand," he said.
"What’s more, this will help children from refugee and multicultural backgrounds to feel welcome and accepted in our classrooms and add value to the education of all our children."
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