Checks were carried out for the Schools Adjudicator, which regulates the admissions system in England.
Of 3,500 faith schools, foundation schools and academies checked, half were breaking a new admissions code.
Chief adjudicator Sir Philip Hunter said many schools were asking unfair questions on application forms such as parents' occupation.
The new code was brought in earlier this year to make the admissions system fairer and more transparent.
Sir Philip was asked by the government to compile a report on school admissions after it found examples of a handful of faith schools breaching the code, for example by asking for donations or to see copies of parents' marriage certificates.
He revealed his interim findings at a conference on admissions in London, as tens of thousands of parents in England apply for secondary school places.
"The Secretary of State correctly identified a series of issues about compliance of the admissions code. He asked me to sort it out," said Sir Philip.
He was "pretty confident" this had been done.
