An inquiry has been ordered following claims that faith schools have been breaking laws aimed at making admissions fairer.
Schools Adjudicator Philip Hunter has been given until July to probe the way all schools and academies decide which pupils to take.
He has been asked by Schools Secretary Ed Balls to ensure all children have fair access to state schools.
Mr Balls ordered the probe after Department for Children, Schools and Families research revealed that a "significant number" of schools in three sample areas were breaking the statutory admissions code.
Breaches included parents being asked for money and personal and financial details.
There have also been continued concerns that faith schools have not been taking enough children who are vulnerable including those with special needs and those eligible for free school meals.
Audrey Osler, research professor at the University of Leeds and director of the centre for citizenship and human rights education, has she was is aware of schools flouting the code, particularly in cases involving disadvantaged children.
She said: "Last summer while travelling around the country doing work for the Runnymede Trust, communities expressed concerns about admissions and particularly that it was the most vulnerable children who are not being considered for faith school places."
Philip Hunter last week wrote to ministers of his concerns that admissions authorities could still be operating unlawful arrangements.
He will give ministers an interim report in July. A full report will be published in September.
The secretary of state is also publishing draft regulations in Parliament which will extend the amount of time local people have in which to object to school's written admission arrangements.
Arrangements for next year's intake have to be published by 15 April.
Mr Balls announced last week that every local authority would be required to monitor admissions arrangements and ensure that children in care and those with statements of special educational need are prioritised as the law says they should be.
He added: "We are acting now to make sure all children have fair access to schools. I know all the major faith groups are committed to stamping out practices which could penalise low-income families or increase social segregation.
"We've made it clear that it is unacceptable not to comply with basic admissions law and we will work with every local authority and faith body to make sure this happens."
In a statement the Catholic Education Service said: "The conduct of admissions arrangements, the right to object to arrangements, and the need to ensure clarity and fairness are critically important. We, therefore, welcome the Secretary of State’s announcement that he is strengthening the requirements in place to ensure that fairness and transparency are achieved in the case of admissions to all types of maintained schools. Our diocesan officers may find it helpful to have the period for objections following consultation on admissions arrangements extended from six to sixteen weeks, as the Secretary of State will now require. This will give diocesan officers more time to work with their schools where necessary.
"We look forward to the Schools’ Adjudicator and local authorities working with the CES and diocesan officers so that together, through our various roles, all parties are helped to fulfil their responsibilities with regard to admissions arrangements."
The Church of England also welcomed the statement. The Rt Revd Stephen Venner, Bishop of Dover and Acting Chair of the Church of England's Board of Education, said: "The Church issued its own fully compliant national guidance more than a year ago and will continue to work with dioceses to ensure that all its schools obey the requirements of the Code.
"Our governing bodies are composed largely of volunteers, committed to making the Admissions Code 2007 work to the benefit of pupils and school, and we are grateful for all that they do.
"The Church of England welcomes the further statement made today by the Secretary of State for Children, Schools and Families. We join him in a determination that all schools should fully implement the Admissions Code and believe that revised Regulations to allow a further period for objection to admission arrangements will reinforce existing law and guidance."
But Jonathan Bartley, co-director of the religious thinktank Ekklesia, who has just recently won a year long battle to get his own son who has special needs into a church school said: "Church schools should be leading the way in taking the most vulnerable children. Instead, there is a mounting body of evidence that such schools are taking far fewer.
"Church schools, although funded almost entirely by the taxpayer, still seek control their own admissions arrangements - which usually favour children of church-goers before anyone else in their community. This sends off a message - not of care for the most vulnerable - but of being a self-serving club that cares first and foremost about its own."