Proposals that were feared would give funding chiefs the power to oust vice-chancellors from office have been redrafted following strong opposition from the academy.
The Higher Education Funding Council for England has made a "substantive change" to its controversial plans for the financial memorandum - its funding agreement with universities.
A draft version of the proposal suggested that the "designated officer" responsible for ensuring that the terms of the funding agreement are met - usually the vice-chancellor - should be renamed the "accountable officer". The document went on to state that "in exceptional circumstances", a governing body would need to appoint a new accountable officer if the original "cannot be relied upon".
It followed last year's stand-off between Hefce and London Metropolitan University, which eventually led to vice-chancellor Brian Roper and the institution's lay governors being forced to step down over inaccuracies in the student-data returns supplied to the funder.
Papers from Hefce's most recent board meeting in May show that it received responses from 85 per cent of universities on the proposals for the financial memorandum - with 78 per cent objecting to the "accountable officer" plans.
The papers say that most of the opposition related to a "misperception that Hefce was claiming the right to instruct a governing body to dismiss its vice-chancellor". However, they add that the "requirements" in relation to the accountable officer have been redrafted.
Details of the changes will be made public after the final memorandum is approved by Vince Cable, the business secretary, in time for its implementation on 1 August.
The board papers also show that the vast majority of institutions have rejected proposals to include the subject of academic quality in the financial memorandum.
More than 80 per cent of the replies oppose the proposition, with most universities worried that responsibility for standards would be transferred from academic boards and senates to governing bodies.
According to the papers, Hefce has "no intention" of transferring such powers, but again the final document has been amended in light of the concerns raised by the sector.