Edinburgh was the only Scottish institution to improve its standing in the Times Higher Education World University Rankings.
But Glasgow, Aberdeen, St Andrews and Dundee all saw their ratings drop dramatically.
The editor of the ratings warned UK universities were in danger of falling behind Asian rivals.
The California Institute of Technology retained the top spot in the survey - with Oxford University coming in second.
The UK was the second best represented country overall in the rankings, and three English universities were in the top ten.
But while the University of Edinburgh climbed from 36th to 32nd, Glasgow University fell 37 places to 139th, while Aberdeen dropped 25 places to joint 176th.
St Andrews went from 85th to 108th, and Dundee fell out of the top 200 altogether.
A spokesman for the University of Dundee said: "While we are disappointed with the drop in our overall position in the Times Higher Education World University Rankings, it is important to look at the context.
"Dundee actually recorded a slightly higher overall score than last year, according to the metrics used in the table. This includes higher scores for teaching, international outlook, and research."
Education Secretary Mike Russell said: "Scottish universities are well known around the world for the quality of education they offer.
"We have invested significant funding in our universities to ensure they can continue to offer a world-class degree and compete internationally.
"We will continue to deliver access to university based on the ability to learn, not the ability to pay, and this year more students will be studying at our world-class universities - unlike universities in England where, overall, the number of acceptances has fallen."
However, Scottish Labour MSP Hugh Henry said: "Despite generous settlements for universities paid for with money from Scotland's hard-pressed colleges, this clearly shows that Scottish universities are facing major challenges both within the UK and internationally.
"Many universities are privately concerned about how their funding will be sustained in the future.
"We need an open and honest debate about how Scotland's universities can compete internationally whilst properly funding Scotland's colleges."
While the US and the UK still dominated the ratings, significant gains were made by their top Asian competitors.
The editor of the survey, Phil Baty, said uncertainty in education in England could see world-class universities collapse into global mediocrity.
He added that while Scotland was better protected by current policies, those were unlikely to be enough to meet the challenge posed by massive spending in Asia.
Mr Baty told BBC Radio Scotland's Good Morning Scotland programme: "We have to look at ways to ensure that in times of austerity we're getting money into our universities.
"I actually think the tuition fees that have been tripled in England aren't enough to cover the gaps in funding in other areas like research. Scotland's done well to protect higher education funding but it's not really enough."
Alastair Sim, director at Universities Scotland, said having four Scottish universities in the world's top 200 was a "recognition of the strength of Scotland's higher education sector".
He said: "It is clear that the value of a Scottish higher education stands up to international comparison.
"However, Scotland's universities are competing in a brutally competitive global marketplace. It will take the continued commitment of energy, initiative and investment if we want to compete with the increasingly powerful top Asia-Pacific universities and the best of Europe and America.
"We are ambitious for a Scottish higher education sector truly excellent in world terms, not just truly excellent when compared to the rest of the UK."
The Times Higher Education World University Rankings employ 13 separate performance indicators, which it says makes it the only world rankings to examine all the core missions of the modern global university - research, teaching, knowledge transfer and international activity.
Scottish universities have slipped down an annual list of the world's top 200 institutions.