Church of England schools were also included in the study that found children as young as three are wearing the head scarf.
Michael Nazir-Ali, a former Bishop of Rochester, told The Times that Muslim headwear should not be a part of school uniform.
He added: "If there are difficulties, they can be negotiated on a case-by-case basis between parents and schools."
Opponents to the policy believe that allowing religious headscarves creates division in classrooms.
They have also questioned why the policy is in place because Muslim girls traditionally don't wear hijabs until puberty. According to The Times there are fears young children wearing hijabs sexualises them.
Gina Khan, a children's rights campaigner in Birmingham, told The Times: "Schools are allowing it because they are afraid of being called Islamophobic and they have been told that this is a religious garment, but they need to support Muslim girls to have free choices, not to be set apart from other children."
According to The Times, 46 per cent of 72 primaries surveyed allowed the hijab in Birmingham, with 36 per cent in Luton and 34 per cent in Tower Hamlets.
Dame Louise Casey, a government official working social welfare told the paper she mediated a disagreement in Birmingham when a Catholic school felt pressured to allow a four-year-old girl wear a head covering.
According to The Times, The Department for Education said that it is up to schools to address the matter of uniforms.