Three newspaper tables and two world rankings were analysed for the Higher Education Funding Council for England.
The researchers said efforts to move up the tables might clash with policy objectives and academic standards.
University leaders say there is still insufficient transparency about the way that the league tables are compiled.
The study was undertaken by the Centre for Higher Education Research and Information at the Open University and Hobsons Research.
They looked at the Sunday Times Good University Guide, the Times Good University Guide, the Guardian University Guide, the Academic Ranking of World Universities published by Shanghai Jiao Tong University Institute of Higher Education and the Times Higher Education Supplement (now THE)/Quacquarelli Symonds ranking.
Their report, Counting what is measured or measuring what counts?, published by Hefce during its annual conference, said there was clearly a demand for league tables among prospective students and others.
It said the rankings largely reflected "reputational" factors such as students' qualifications on entry, the level of degree they attained and Research Assessment Exercise grades.
The tables measured the data available, some of which were poor indicators for the qualities they were supposed to reflect such as "excellence" or "a world class university".
"Also the weightings applied do not always seem to have the desired effect on the overall scores for institutions.
"This brings into question the validity of the overall tables," the report said.
"The resulting rankings largely reflect reputational factors and not necessarily the quality or performance of institutions."
