Most of the concerns are centred on moves to ban heads from selecting children based on the position that schools are placedJ on application forms.
At the moment many faith foundation and grammar schools operate the so-called "first preference first" rule favouring children who list a certain school at the top of their application.
Many church schools use this as a test of pupils' commitment to a faith-based education, saying they cannot be serious if they place a faith school as their second or third choice.
Currently, the rule is not banned, although the Office for the Schools Adjudicator, the independent admissions watchdog, has consistently taken a hard-line on first preference first.
In the past two months 15 Roman Catholic and five Anglican schools have been ordered to stop using the policy after complaints were made to Peter Matthews, the adjudicator, .
The John Fisher secondary in Sutton, south London, was criticised last month by Mr Matthews who said the continued use of first preference first was inhibiting parental choice by seeking a "premature commitment" to a certain school.
Richard Challoner Catholic boys' school in New Malden, Surrey, was also criticised by the adjudicator in July, after Kingston borough council objected to its use of first preference first.
But this week Tom Cahill, headteacher, defended the policy. "The families most committed to the school and the faith should be the ones who get places," he said.
"They ought to have priority over others. Commitment from parents makes a huge difference as you know they will really give support to their child and the school."
He said parents expected their first choice school to carry more weight in the application process.
The new admissions code, published last week, will be open to consultation before becoming into force next February.
It was heralded by Alan Johnson, the education secretary, as an end to "any selection by stealth".
Under the new rules, faith schools must be clear how religious affiliation is to be judged and will be banned from interviewing pupils.
It could prompt another row between ministers and the London Oratory school, the Catholic secondary where Tony Blair sent three of his children.
The school won the right to continue interviewing following a High Court battle in 2004.
Headteachers will also be banned from picking children whose parents contribute money to the school and uniforms must not be overpriced. Costly uniforms have sometimes priced some parents out of certain schools.
Canon John Hall, chief education officer for the Church of England, said he supported the majority of the code.
But he insisted the first preference first rule should be employed to stop Anglican schools acting as a fall-back when parents fail to get their children into local grammar schools.
Chris Waterman, executive director of Confed, which represents council education directors, said: "Faith schools should open their admissions policies to independent scrutiny. They still have the right to select pupils along religious lines if that's what they want, but it should be an objective and transparent process."
The TES revealed last week that faith schools and foundation schools, which currently control their own admissions, were among the most socially-selective schools in the country.