Officials have told ministers that changing the law would be a legislative nightmare as many universities are set up by Royal Charter and have a history of fiercely - and successfully - defending their autonomy.
Their official position - in advice to students - is that "top-up fees play no part in the Government's proposals. No university or college should proceed on the basis of introducing such additional fees."
A spokeswoman for the Department for Education and Employment did not rule out future action to ban top-up fees.
Universities will collect the fees, and will be responsible for any student whose parents refuse to make up their contribution to tuition - but there will be no legislation to force parents to help their children with fees.
The decision ends the stand-off between the Government and the universities over the collection issue. Martin Harris, chairman of the Committee of Vice Chancellors and Principals, said this week: "The Government has determined that fees from full-time home undergraduate students should be collected by the universities and CVCP has accepted that."
Details about how some of the new scheme will work have also been clarified. Students on PGCE courses will be exempt from the Pounds 1,000 fee because, "as employers of teachers in the public sector the Government has a key interest in the effective training of teachers and in maintaining a healthy supply of teachers."
Medics and dentists will pay fees only for the first four years. After this, non-repayable bursaries, assessed against family income, will be available to meet living costs. Health departments will continue to provide bursaries and meet tuition fees for students on eligible courses - such as trainee nurses - as at present.
A student spending an entire year on a sandwich placement will pay a maximum Pounds 500 a year, assessed against family income. If the placement is less than a full year, the Pounds 1,000 is payable.
The Government says that longer courses entail bigger costs and therefore the graduate should contribute. It says: "Students applying for courses will need to consider carefully the advantages of an extra year alongside the extra contribution which they may have to incur as a result."
Access courses are FE courses and are not eligible for a mandatory award or student loan. A student who begins a degree course in 1998 or 1999, immediately after an access course, will be treated as a new entrant to higher education and therefore liable to fees.