Just two universities – St Andrews and Edinburgh – said they would refund students in university accommodation forced to stay at home to abide by Scottish Government guidance.
It came as Edinburgh University also told students they may not be able to return to campus until February 12, more than a month after teaching will restart.
Responding to queries on the staggered return, most universities said decisions on refunds and on the timing of students returning were yet to be made.
The Scottish Government is under growing pressure to either fund the refund of student rents themselves or to provide universities with the cash to do so.
Scottish Conservative education spokesman Jamie Greene called on the Scottish Government to “pick up the tab” until students are able to return to campus.
He said: “It seems illogical and entirely unfair to ask students to pick up the tab for university accommodation which they have been told not to return to.
“The Scottish Government should stop hiding behind universities, a sector already on knees after years of chronic underfunding”
Scottish Liberal Democrat leader Willie Rennie echoed the calls due to the “immense disruption and upheaval” students face.
He said: “This is not just an issue that affects halls of residence. Ministers also need to consider those students who live in private accommodation, who will be unable to access their property and their possessions as a result of the government's proposed staggered return.”
Andrew Wilson, a former president of Edinburgh University’s Student Association, said the decision to stagger a return could lead to students ignoring the guidance and called for rent rebates for all students without face-to-face teaching.
The psychology student said: “After a first semester where I had no face-to-face teaching at all, even after being promised hybrid learning by the university, I am now being told that I should not return to Edinburgh until February 1, despite having a flat I have to pay £530 a month for.
“This is yet again another example of students being disregarded and mistreated by their universities and the Scottish Government more generally.
"My worry is that students will completely ignore this guidance, having to move back because of the financial pressures, and there will be no mass testing capacity to support their return to university communities.”
Scottish Labour’s education spokesperson Iain Gray said: “It is incumbent on all universities to ensure that no student is hit in the pocket for accommodation that they cannot reside in. The Scottish Government needs to outline how it will support universities to refund students appropriately.”
The calls follow Universities Scotland claiming a staggered return could lead to “major cost implications” linked to accommodation for universities “under very serious financial pressure”.
A Scottish Government spokesperson said it had no “direct role” in student accommodation and that decisions must be made by universities themselves.
They added: “Where applicable, however, we do encourage accommodation providers to come to an appropriate resolution of issues around tenancy agreements and rent payments.
“We are discussing these issues with Universities Scotland and the NUS.”