The latest Times Higher Education index has moved its top five Australian universities down a few spots, sending some authorities into an explanation-finding spree.

The five Australian universities that made it to last year’s top 100 World Reputation Rankings list have all fallen in this year’s ranking.

Only the University of Melbourne remains in the top 50, with the University of Sydney and the Australian National University falling from the top half, and the University of Queensland and University of New South Wales still managing to make the top 100 cut.

Monash University has been dropped from the list this year.

Universities judge universities for adherence to the core mission, combined with 13 performance indicators in five areas: teaching, research, knowledge transfer and international outlook.

Universities are not eligible for ranking if they do not teach undergraduates, if they only teach a along narrow subject lines, or if they produce fewer than 200 research articles per year.

Accolades have been rained on Macquarie University and the Australian National University, which have made the top 10 list for most international university. Macquarie was ranked first in the world.

Times Higher Education editor Phil Baty says around $2.8 billion in cuts from Australia's tertiary sector have affected local universities.

“We can't read their minds but we've been speculating that the funding cuts announced by the former government, unprecedented cuts, sent some very negative messages out there into the world,” he said.

The cuts mentioned were from April last year, when the federal Labor government pulled billions fromuniversity research funding to add to the pile for Gonski reforms.

“That money is coming out of our system, it means there are less researchers than there were, less researchers supported and that has consequences,” University of Melbourne vice-chancellor Glyn Davis has told the ABC.

“One of the distressing things is how long those consequences tend to linger. Once you're seen as no longer performing to a global standard, it's very hard to win back the standing that you once had.”

“They are pretty powerful signals that Australia, already a very low investor of public money in higher education, is going to invest even less and people read this.”