Cambridge and Oxford remain in the top five, at fourth and fifth place respectively, but both have moved down two places on their 2015 ranking.
The US dominates the Times Higher Education (THE) reputation rankings, with Harvard and MIT in top places.
Asia has 17 universities in the top 100 - up from 10 in last year's rankings.
The highest rated Asian universities are the University of Tokyo in Japan in 12th place and China's Tsinghua University in 18th place and Peking University in 21st place and the National University of Singapore in 26th place.
These are rankings based on reputation and perceived status, based on the opinions of an international panel of academics.
These are separate from the university rankings based on research and teaching quality.
Three London universities stay in the top third of the reputation table - Imperial College London at 15, University College London at 20 and the London School of Economics and Political Science at 24 - but each has fallen slightly on last year's ranking.
University of Edinburgh (38th), King's College London (43rd), University of Manchester (joint 49th), London Business School (between 81st and 90th) and University of Warwick (between 81st and 90th) also made the top 100 global reputation ranking.
The University of Bristol and Durham University have fallen out of the top 100, bringing the UK's total number of universities in the rankings to 10 for 2016 - down from 12 last year.
The 10 top institutions by reputation are:
1.Harvard University, US
2.Massachusetts Institute of Technology, US
3.Stanford University, US
4.University of Cambridge, UK
5.University of Oxford, UK
6.University of California, Berkeley, US
7.Princeton University, US
8.Yale University, US
9.Columbia University, US
10.California Institute of Technology, US
Diminishing performance
THE rankings editor Phil Baty said the UK had lost ground this year.
Even the country's most prestigious institutions have slipped, with the universities of Cambridge and Oxford each dropping two places to fourth and fifth place respectively," he said.
The UK's diminishing performance occurs as institutions in Asia rapidly rise up the table - the continent has 17 representatives, up from 10 last year.
Mr Baty said cuts to higher education funding and a series of immigration measures affecting overseas students were "starting to have an impact" on the UK's global reputation.
The UK will have to ensure that it can still draw in talent and investment from across the world and it does not lose its position at the heart of higher education's global elite," he added.
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