Sweden's placement of three institutions on the Times Higher Education's 2013 World Reputation Rankings places it in a tie for sixth place overall with Hong Kong and Canada, and just behind France, which has four universities among the top 100.
The results are based on a survey of senior academics, providing what the publication refers to "the only global index based purely on the power of university brands".
Karolinska Inistitutet outside of Stockholm was the highest ranked Swedish university, landing in the 61-70 band.
However, the report's authors cautioned that Sweden's universities are "losing global status".
"There are alarming signs that [Sweden] is losing its lustre. None of the country's three representatives make the world top 50; indeed, all have lost ground this year," Times Higher Education Rankings Editor Phil Baty said in a statement.
Baty singled out Uppsala University as "the greatest cause for concern", noting the school ranked in the 71-80 band in 2012 band "but now barely makes the top 100".
When asked about the drop, Uppsala University Deputy Vice Chancellor Anders Malmberg had mixed reactions on the institution ranking.
"Uppsala strives to be among the world's top internationally-oriented research universities. We think we should be included in such rankings and are happy to belong to that top-100 group," he told The Local.
"But we are never satisfied when we see our position fall and want to continue working on strengthening our research and education programmes."
He added, however, that the university places more emphasis on "indicator-based" rankings rather than "reputation-based" ones, which he said are "harder to analyze".
"You never want to put too much emphasis on any one ranking but we have to keep an eye on them whether we like it or not," he added.
Malmberg said it was unclear whether or not Sweden's recent introduction of tuition fees for non-EU university students factored into the lower rankings.
"We certainly lost a lot of non-European students and need to work more with how we develop and market our programmes," he said.
Meanwhile, University Chancellor Lars Haikola, who heads the Swedish Higher Education Authority (Universitetskanslersämbetet), downplayed the significance of the rankings.
"We don't put much faith in rankings here in Sweden," he told The Local.
"Swedish universities maintain high quality when it comes to their teaching and research programmes."
Haikola explained that Sweden is one of the only countries that has boosted research spending at a time when global economic troubles have prompted many country's top slash research budgets.
"We're spending billions [of kronor], but the initiatives are being carried out in a long-term perspective," he explained.
He added that any drop in the rankings by Swedish universities was "relative", but agreed that the rise of universities in Asia posed a challenge.
"It's a challenge for all countries to remain at the top," he said.
"It's hard to compete and Asian universities have taken great strides."
However, Haikola emphasized that he wasn't worried about any perceived drop in reputation for Sweden's universities.
"Worry is too strong a word," he said.
"Certainly, we must be aware of what's happening and what sorts of efforts are being undertaken elsewhere, but it's important not to exaggerate the significance of these figures."
The 2013 rankings are based on more than 16,000 responses to a survey conducted in 144 countries in March and April 2012. The respondents had been working in the academy for 17 years on average.
The United States dominated the World Reputation Rankings, snagging seven of the top ten spots and 43 of the top 100, with Harvard University maintaining its hold on the number one spot, followed by the Massachusetts Institute of Technology (MIT).
Cambridge and Oxford universities in the UK ranked three and four, respectively, with the University of Tokyo landing in eighth place as the top-ranked Asian university.