Edinburgh is listed 16th in the 2013 Complete University Guide, three places lower than before, while Glasgow has climbed four places to 17th.
St Andrews had the highest ranking of any of the Scottish universities at number six in the league table, the same as last year.
Heriot-Watt came in at number 40, two down from last year; Queen Margaret at 84, three up from last year and Edinburgh Napier at 91, down from 84.
However, in a separate listing for subjects offered, Edinburgh was in the top ten for 23 out of 48 subjects, coming top in nursing.
Dr Bernard Kingston, author of the guide, said the impact of the economic downturn on graduate job prospects had affected this year’s table.