Elizabeth Passmore's final report before retirement complains admissions are too often "unnecessarily complex", "unfair" or unclear.
Schools which are their own admissions authorities, like academies or faith schools, are more likely to be at fault, says the report.
The government said it would review the findings and take action where needed.
England's School Admissions Code requires places to be offered in a fair and open way, with arrangements set out so that parents can "understand easily how places for that school will be allocated".
Admission arrangements run by local authorities for community and voluntary controlled schools "are almost always clear and uncomplicated so it is easy for parents and others to understand how places will be allocated" says the report, published late last year.
But "the complexity of some schools' admission arrangements continues to be a matter of concern," writes Dr Passmore.
"The arrangements set by some own-admission authority schools have so many levels of priority that often it is unclear how the arrangements could actually be applied."
These complex arrangements can include numerous oversubscription criteria, different sub-categories of places, more than one catchment area, feeder schools, banding tests and aptitude assessments, says the report.
"The complex arrangements of some schools do not serve local children well," adds Dr Passmore.
Too often, says the report, admission arrangements are hard to find on school websites or not published at all, while some faith schools ask parents to fill in supplementary forms, asking for information prohibited under the code.
Dr Passmore says banding tests are proving a particular problem.
Schools say they use them to ensure a comprehensive intake but the report suggests they can be used to increase numbers of higher ability pupils.
"Children living near the school, but placed in a band with many similar children, may not be allocated a place," says the report.
"The first hurdle in gaining a place is to take the test."
These tests are also expensive, up to Â£500 per child to administer, and the report questions the effects of banding on children, its purpose and costs.
Dr Passmore also said she was "surprised and concerned" by an increase in schools operating as their own admissions authorities employing lawyers when they receive objections to the criteria they use to admit children.
"Schools should be able to construct lawful arguments to their arrangements without recourse to legal advice," she writes.
Overall the report notes the adjudicator dealt with 218 admissions cases in 2014-15, down from 274 the previous year, but the number upheld or partially upheld rose to 159, from 99 in 2013-14.
And local authorities withdrew 284 offers of school places because of fraud, up from 186 the previous year.
Margaret Tulloch of the Comprehensive Futures campaign group described the report as "very disturbing" and called for a "wholesale review of school admissions".
"She is right to raise concerns about own-admission authority schools failing to meet the requirement of the code and about so-called fair banding.
"These problems will only increase as more schools become academies."
A Department for Education spokesman said the government wanted every child to have the opportunity of going to a good local school.
"The chief adjudicator's annual report helps us identify how we can continue to improve the admissions framework to ensure fair access for all children.
"We will review her findings and take action where appropriate." said the spokesman.
Too many schools in England break the rules on admissions arrangements, says the outgoing chief schools adjudicator.