The Education Secretary Charles Clarke says private school head teachers are misguided in their boycott of Bristol University over its admissions policy.
He says the head teachers would be better off talking to Bristol about their concerns.
On Tuesday, a group representing head teachers at independent schools advised its members not to encourage sixth-formers to apply to Bristol.
The Headmasters' and
Headmistresses' Conference (HMC) and Girls Schools' Association (GSA) accuse Bristol of discriminating against students from private schools and good state schools in favour of children from disadvantaged areas.
The university denies positive discrimination.
Mr Clarke said: "I think HMC and GSA are misguided in the approach that they are following."
Asked what the private schools should do, he said: "Talk to Bristol - have a mature conversation".
But HMC chairman Graham Able, the head of Dulwich College said there had already been a lot of talks.
"We have been in negotiations with Bristol for the last 12 months and it is the opinion of our chairs of university working parties that they were given assurances by Bristol that have turned out to be lacking in substance," he said.
Mr Able continued: "I can give you many examples of working-class pupils who
have gone to Dulwich College on free places and have gone to top universities.
"It would be ironic if any of these were to be turned down by Bristol and a
student from a less well performing school was accepted instead."
At Prime Minister's Question Time in the Commons on Wednesday, Tony Blair defended the government's goal of getting more children from poorer backgrounds into university.
But he insisted places should always be given on merit.
"It should, of
course, be based on merit and it should be based on the ability of students.
"But we should do everything we possibly can, subject to what I have just said, to widen access into our
universities because it is also important that we allow children from working
class and poorer backgrounds the chance of a first-class, quality, university
Mr Clarke's comments were made during a briefing for journalists.
He told them A-level grades, while important were not the absolute guide to university entrance.
It was also important to look at a range of other indicators of ability, motivation and interest.
The general secretary of the National Association of Head Teachers (NAHT) said the groups behind the boycott were "shooting themselves in the foot".
"HMC and GSA are guilty of gesture
politics of the worst kind," he said.
"Their stance will only serve to damage the interests of their bright
students. There are other means by which any complaints about Bristol
University's admissions procedures can be resolved."
Bristol also has the support of Sir Howard Newby, chief executive of the Higher Education Funding Council for
One of his organisation's roles is to give money to universities for use in
attracting more working class schoolchildren into higher education.
Sir Howard, who was giving evidence to the Commons Education Select Committee,
said: "I'm satisfied that the admissions procedures of Bristol University are
fair and equitable."