The universities of St Andrews, Glasgow and Aberdeen have all slipped down the rankings, while Dundee has dropped out altogether.
Edinburgh University is the only Scottish institution to have improved its position – rising from 36th to 32nd in The Times Higher Education World University Rankings 2012/13.
Phil Baty, editor of the Times Higher Education rankings, warned the Scottish decline was part of a UK-wide issue, with universities facing "a collapse into global mediocrity" as a result of the rise of universities across Asia.
This year, Chinese universities including Peking and Tsinghua, as well as institutions in Singapore and the Republic of Korea, all climbed the tables following significant investment.
"The huge investment in top research universities across Asia is starting to pay off. Some Scottish institutions have fallen far," said Mr Baty.
"While there are current policies protecting investment in universities, they are unlikely to be enough to meet the challenge posed by massive spending in the East. These disappointing results may resurrect the debate about charging tuition fees in Scotland."
The findings mirror those of a report issued by the European Commission last year which stated: "Europe is no longer setting the pace in the global race for knowledge and talent, while emerging economies are rapidly increasing their investment in higher education."
A spokesman for Universities Scotland, which represents university principals, said the tables showed Scotland was still punching above its weight – but he stressed the need for continued funding to stay competitive.
"With four Scottish universities in the world's top 200, we welcome the recognition of the strength of Scotland's higher education sector," he said.
"It is clear the value of Scottish higher education stands up to international comparison, but 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."
Professor Sir Timothy O'Shea, principal of Edinburgh University, said: "Our position in the rankings highlights the university's standing, both in the UK and the wider world, and recognises our excellence in teaching, research and graduate employability."
A Scottish Government spokeswoman said: "Although we are disappointed to see slight falls, we are confident our universities are still offering an excellent quality of education.
"We have invested significant funding in our universities to ensure they can continue to offer a world class degree and compete internationally."
Despite the decline in many institutions' positions, the UK still has the second-best university system worldwide.
In total, 10 UK universities are in the top 100 in the rankings compared with 12 last year and 14 in 2010/11. The latest table shows the UK has three universities in the top 10, with Oxford taking second place, up from fourth last year.