The universities of Edinburgh, St Andrews and Aberdeen dropped in the Times Higher Education World University Rankings for 2013-14.
Aberdeen slipped from 176th place in 2012-13 to 188,Edinburgh dropped seven spots to 39 and St Andrews fell nine places to 117.
In contrast, Glasgow rose 22 places to 117 and Dundee re-entered the top 200 at number 196.
The rankings rate universities worldwide on 13 measures including teaching, research and their international outlook which includes the number of overseas students and staff they have.
Their publication contrasts with last month's annual QS World University Rankings which names University of Edinburgh as one of the top 20 universities in the world.
The institution climbed four places, from 21 to 17, in the QS league table while University of Glasgow rose three places from 54 to 51 and University of St Andrews climbed 10 places to 83.
A spokeswoman for University of Edinburgh highlighted its QS ranking, stating: "University league table places change constantly and we need to view them in the light of these fluctuations, while also bearing in mind that different tables use different criteria on which to judge institutions."
A University of Aberdeen spokesman said league tables are calculated using different criteria and indicators.
"We are pleased to have both maintained our position as a top 200 university in the Times Higher Education world rankings, and to have risen 14 places into the top 150 in the recent QS world rankings," he said.
Rankings show only a small part of the student experience and Aberdeen University has invested heavily in its campus and a reformed curriculum over recent years, the spokesman said.
University of Glasgow welcomed its "dramatic" rise up the table.
"This confirms the reputation of Glasgow as a world-leading research intensive university where the student experience is second to none," a spokesman said.
Professor Pete Downes, principal of University of Dundee, said: "I am pleased to see the Times Higher Education rankings recognise the quality of Dundee as an institution as ranked against our peers around the world.
"Getting into the top 200 individually ranked universities is an accolade coveted by institutions across the globe and demonstrates that we meet the most exacting standards of excellence."
Education Secretary Michael Russell said: "Scottish universities are known at home and abroad for their excellence and this is highlighted by the fact that five of our universities feature in these international rankings. Scotland has the most universities per head of population which clearly shows we continue to excel and build on our unrivalled record of success.
"Taken together with the recent QS ratings, it demonstrates that our substantial investment in higher education, over £1 billion annually, is paying off and, most importantly, delivering exceptional opportunities for students and employers.
"Earlier this year we announced additional funding, based on the levels of world-leading research. I am sure the commitment and dedication of our universities and their staff, helped by our funding, will ensure our higher education system continues to go from strength to strength."
Universities Scotland director Alastair Sim said: "Everyone in Scotland can celebrate the fact that we have more universities in the world's top 200 per head of population than any other nation, making us one of the strongest higher education systems in the world.
"Every Scottish institution is engaged in world-leading research, uses innovative learning and teaching methods and looks to make a strong contribution locally, nationally and internationally."