Ed Balls said breaking school admissions rules is "unacceptable"
Almost one in six schools checked by an official inquiry are breaking the code on admissions, ministers have said.
Of the 96 schools in three areas found to be breaking the rules, six asked parents to make financial commitments as part of the admissions process.
Many of the other cases - in England - involved not giving due priority to children in care or with special needs.
Schools Secretary Ed Balls said the situation was "unacceptable" and plans to tighten the rules still further.
Amendments to the Education and Skills Bill, currently before parliament, will:
- require local authorities to report annually on the legality and fairness of all schools admission arrangements in their areas
- extend the power of the schools adjudicator to amend arrangements that come to his attention
- make sure that parents and local communities are properly consulted about school admissions arrangements
Last month the government claimed "a significant minority" of schools in three areas were still breaking the admissions code which was tightened up last year.
It has now revealed that of the 570 schools it checked in Manchester, Northamptonshire and Barnet, some 96 were in breach of the code.
The three areas were chosen as being representative of a metropolitan authority, a shire county and a London borough - and were areas where there had not been objections to admissions policies.
"We have no reason to think that these areas are any different from any other authorities around the country," Mr Balls said.
At the time it declined to put a precise figure on the number involved, pending checks.
Now that the schools have been asked to explain themselves, the Department for Children, Schools and Families has published lists of those involved along with their breaches of the code.
About a third failed to comply in more than one respect.
The schools were allegedly asking parents banned questions about their marital status, financial background or even in some cases asking for financial contributions.
It was put to Mr Balls that he had made too much of these requests for money - that they involved only six, mostly Jewish, schools in Barnet and these were only about 1% of those checked.
Mr Balls said one school would mean hundreds of parents affected, six schools meant thousands.
"I think one child and one parent being deterred from applying to a school because of an unlawful charge is wrong," he said.
"What we are highlighting here is thousands of parents being put in that position."
He rejected the idea that the sort of middle class parents schools wanted to attract could afford the payments - which he said in one of the schools in Barnet were £995 per child per term.
He knew parents wanted the best for their children and he was on their side, "but you can't have a two-tier system".
To eradicate educational disadvantage it was "absolutely critical" that governing bodies, local authorities and the Schools Adjudicator enforce the code.
Shadow Schools Secretary, Michael Gove said: "Ed Balls started a witch-hunt against schools which were alleged to be handing out places for cash.
"But there's no evidence that money played any part in determining admissions in any of these schools.
"Ed Balls knows that many faith, and other, schools ask parents if they'd like to make purely voluntary contributions.
"He also knows that Jewish faith schools have to secure additional funding to guarantee the physical safety of their children.
"But he put these schools in the dock simply in order to distract attention from the fact that 100,000 parents weren't getting their first choice of school thanks to his policies," he added.