In a survey of eleven areas across England, the Sunday Times found Church of England primaries in six regions included the hijab in their uniform policy.
The covering is only typically worn by girls once they reach puberty in their teenage years and the latest revelations have sparked fears young Muslim girls are being sexualised.
Anglican figures appeared divided over the issue, with former Archbishop of Canterbury Lord Carey telling the Sunday Times such school policies should be "fiercely resisted".
In contrast, Bishop of Bradford the Rt Rev Toby Howarth dismissed concerns, saying: "This is a matter of religious identity, not sexualisation."
Ofsted said it is investigating whether head teachers are coming under undue pressure to include hijabs in their uniform policies. The education regulator cited "growing concern" over the trend.
The Sunday Times found 18 per cent of the 800 primary schools it surveyed list the hijab in their uniform policies. Of the 17,000 primaries across England, the overall figure is likely to be in the thousands.
In response, the Department for Education told the paper: "If a school decided to allow a pupil to wear a burqa, that would be up to the school."