Universities based in the US dominate the top 20 in the global annual rankings with Harvard ranking first yet again.
Only three non-American institutions made it into the top 20, all from Europe, including Britain's Cambridge in fifth place and Oxford in 10th in the 2013 Academic Ranking of World Universities.
The highest-ranked continental European university was the Swiss Federal Institute of Technology Zurich in 20th position.
The rankings are compiled by a research centre that is part of Shanghai's Jiaotong University.
They have been criticised in the past for emphasising scientific research while neglecting the humanities.
Harvard University has been in the number one position since 2003, when the survey began.
The top five for 2013 also include Stanford, University of California at Berkeley and the Massachusetts Institute of Technology (MIT).
The top 10 also includes the California Institute of Technology, Princeton, Columbia and the University of Chicago.
The top 10 is virtually unchanged from last year with only Berkeley and MIT changing places.
The rankings, which survey more than 1,200 universities and pick the top 500, are based on six indicators.
They include Nobel Prize and Fields Medal winners, the number of "highly cited" researchers and the number of articles by faculty published in the magazines "Nature" and "Science".
The top-ranked universities in the Asia-Pacific region are the University of Tokyo at 21, Kyoto University at 26 and the University of Melbourne, at 56.
A number of Chinese institutions made the top 200, with Shanghai's Fudan University overtaking prestigious Peking University as the mainland's best-rated institution.
Jiaotong itself was ranked third in mainland China, and at 167 overall.
The list was originally conceived to benchmark the performance of Chinese universities, as China seeks to build world-class research institutions.
But some European officials have said the criteria underemphasise the humanities and are thus biased against Europe's universities.
The Center for World Class Universities at Shanghai Jiaotong University, which released the rankings, defended the survey as transparent and reliable.
"It has been recognised as the precursor of global university rankings and the most trustworthy one," it said in a news release.