Universities could face legal action as a result of the white paper, according to experts.
Garry Attle, a partner in education law at Mills and Reeve, said that new widening-access initiatives could open admissions to legal challenge for the first time.
And an academic lawyer warned selectors that applying the same entry criteria to all applicants could amount to indirect discrimination under human-rights laws.
Lois Bibbings of Bristol University's School of Law said there were moral and legal arguments in favour of making different grade offers to different kinds of students.
Speaking at last week's "Fair Enough?" conference in London, Dr Bibbings said that the European Convention on Human Rights and the Human Rights Act 1998 included the right to education and freedom from discrimination.
"It is arguable that applying the same entry requirements for all students amounts to indirect discrimination because treating all people the same would significantly disadvantage an identifiable group for no good reason.
In such circumstances, different treatment is justified or may even be required precisely because its purpose is to assist a disadvantaged group."
Mr Attle warned that top-up fees combined with new access initiatives meant that the courts, which historically do not rule on academic decisions such as admissions, would now get involved.
The white paper proposes that universities sign agreements with the access regulator promising to recruit more students from non-traditional and poor backgrounds.
"At the moment, when students do not get into university they may seek judicial review of the decision, but if the university can show that the decision was made on academic grounds the courts will not interfere," Mr Attle said.
"But once you bring in any non-academic matters to the admissions process, the courts may well become much more comfortable saying whether the university has got it right or wrong."
Mr Attle warned that students could start to turn to trading standards and consumer protection laws as universities used complex pricing policies for courses.
Dr Bibbings said an applicant with three Bs at A level from a poorly performing school and with no family experience of higher education might be judged to be doing as well as an applicant with higher grades from a top school and with professional parents. This might result in different grade offers.
Far from amounting to positive discrimination, the shift would bring university selection more in line with practices used in employment, she said.
However, there are fears that privately educated students could lose out.
John Dunford, general secretary of the Secondary Heads Association, said there would be opposition to any move that resulted in quotas for state and independent pupils.
"There must be a level playing field and the criteria must be open, fair and transparent," he said.
Dr Bibbings said that as admissions tutors already accepted that exam grades were not the only accurate indicator of ability or motivation, adopting a flexible admissions policy should not be equated with discrimination against privately educated applicants, who in some cases could be offered lower grades.
"In adopting fresh approaches to admissions, elite institutions are arguably recognising and seeking to address a history of discrimination in favour of applicants from the independent sector."