Ruth Kelly has said there is "no way" that plans to create more independent state schools will mean a return to selection by ability in England.
Ms Kelly said she and Mr Prescott shared 'the same values'
The plans would help create a "fairer" society, the education secretary told the Commons education select committee.
Deputy Prime Minister John Prescott has said giving schools more say over admissions could adversely affect children from poorer backgrounds.
But Ms Kelly said she, Mr Prescott and Tony Blair shared "the same values".
The plans would allow local education authorities a more strategic role, monitoring standards and commissioning services rather than running schools.
Schools could become "trusts", with more say over admissions, finances and staffing.
Conservatives have urged the government not to "water down" reforms, which may need their votes to get through the Commons.
The prime minister should ignore Mr Prescott's "class war" worries, they say.
More than 70 Labour MPs have signed alternative proposals that would give local authorities extra powers to co-ordinate admissions.
Ms Kelly has insisted the plans do not mean a return to selection by ability.
On Sunday, Mr Prescott told the Telegraph: "I'm not totally convinced major reform is necessary."
He defended comprehensive schools and warned against any move that could pave the way for their abolition.
He said of the White Paper: "Since I was an 11-plus failure, since I do believe that produced a 'first-class/second-class' education system, I fear this is a framework that may do the same."
Ms Kelly told MPs: "Well I don't agree with him. I think this is a good set of proposals that will help the most disadvantaged children in the most disadvantaged areas as well as contribute to rising standards across the board."
But she conceded: "It is clear that I have a job to do to persuade you and others that is the case.
"I am completely convinced that this will not create a two-tier system - in fact the reverse."
There was a lot of "misunderstanding" of the Education White Paper, published earlier this year, she added.
Shadow education secretary David Willets said Mr Prescott was fighting old "class war" battles and ignoring young people already denied a good education because of selection by house price.
He told BBC News 24: "The crucial question for Ruth Kelly will be 'is it full speed ahead with reforms as set out by the prime minister or is it lots of clever little manoeuvres to water down some proposals, and back-tracking?'"
He added: "We shall see whether she is serious about reform or engaging in a retreat under pressure from Labour's left wing."
Edward Davey, the Liberal Democrats' education spokesman, said: "Ruth Kelly is splitting hairs when she says her White Paper proposals won't increase selection by ability.
"By giving schools the right to set admissions she is taking power away from parents and communities."
Mr Blair has told MPs plans in the White Paper would remain, as they were "the right changes to make".