Schools will be able to ban pupils from wearing full-face veils on security, safety or learning grounds under new uniforms guidance issued by ministers.
Schools Minister Jim Knight says "learning must take precedence"
It says efforts must be made to accommodate religious clothing, but stresses the importance of teachers and pupils being able to make eye contact.
It comes after a girl failed in a legal bid to overturn her school's niqab ban.
Islamic groups have been divided in their response - some "shocked" and others welcoming the guidance.
Headteachers' leaders have applauded the decision, saying that it would provide "clarity" and "reassurance" for schools.
The issue of religious dress has become an increasingly complicated one for schools in recent years, with a handful of high profile court cases over the right to wear a full veil.
A court victory by a Buckinghamshire school (which cannot be named for legal reasons) has prompted the updated guidance.
The school argued the veil made communication between teachers and pupils difficult and thus hampered learning.
Teachers needed to be able to tell if a pupil was enthusiastic, paying attention or even distressed but full-face veils prevented this, it said.
This position was upheld by the High Court - which refused to grant a judicial review - and is expected to form a key part of the guidance.
The guidance says schools need to be able to identify individual pupils in order to maintain good order and spot intruders.
The guidance has divided opinion within the Muslim community
"If a pupil's face is obscured for any reason the teacher may not be able to judge their engagement with learning or secure their participation in discussions and practical activities," it adds.
Schools minister Jim Knight said: "Schools should consult parents and the wider community when setting uniform policy.
"And while they should make every effort to accommodate social, religious or medical requirements of individual pupils, the needs of safety, security and effective learning in the school must always take precedence."
The head teacher of the Buckinghamshire school, who also cannot be named, said it would be very useful to have some clear guidance from the Department for Education and Skills (DfES).
"It's not right that schools should have to be arguing this out case by case," she told the BBC News website.
"Obviously there's a trade-off between schools retaining autonomy over school uniform decisions, on the other hand we will have some very clear guidance from the DfES within which to work."
There were divided responses from the Muslim community.
The chairman of the Islamic Human Rights Commission, Massoud Shadjareh, said he was "dismayed" by the DfES guidance.
Many schools allow Muslim girls to wear head scarves
"Successive ministers dealing with education issues have failed to give proper guidance when requested by human rights campaigners about schools' obligations regarding religious dress, including the head scarf.
"To now proceed to issue guidance against Muslim communities is simply shocking," he said.
But the Muslim Council of Britain's education spokesman, Tahir Alam, said that the new guidance did not "alter the position very much" and said "the vast majority of schools are able to solve these issues locally".
Dr Tag Hargey of the Muslim Education Centre welcomed the guidance.
"When you conceal the face, that actually not only dehumanises the person involved, but also creates a chasm, a gap, a bridge of non-understanding between communities and I think the sooner we can get rid of this veil, this face veiling, this face masking in Muslim societies across Britain, so much the better."
Ayshah Ishmael, a teacher at a Muslim girls' school in Preston who wears the niqab away from the classroom, told the BBC wearing the veil promoted equality.
She said: "You're judged for who you are and not what you are, so I think there are two arguments to the whole equality issue."
The DfES said it was not ordering or advising head teachers to ban the veil, simply confirming that they have the ability to do so if they wish, so long as they carry out proper consultation.
Association of School and College Leaders' general secretary Dr John Dunford said he was pleased the government is supporting school leaders in upholding school uniforms.
"Repeated and blatant breaches of uniform policy undermine the school ethos," he added.