Aberdeen, Abertay in Dundee, Queen Margaret in Edinburgh and West of Scotland said they had a lower income from students from England, Wales and Northern Ireland.
The figures emerged from a Freedom of Information (FoI) request to the institutions.
The biggest loser was Aberdeen, with a shortfall of £1.2 million, while Queen Margaret was down £318,000 and Abertay down £41,000. West of Scotland said its income was "less than previous years".
The issue is important because the decision by the Scottish Government to let universities here charge students from the rest of the UK (RUK) up to £9000 a year was seen as a crucial new income stream.
Although public funding for these students was withdrawn, it was expected that universities would be able to grow numbers to compensate.
The FoI request by student body NUS Scotland shows for the first time the new policy could result in the finances of some universities being damaged as a result of the policy change.
However – although they currently don’t hold the information requested – it is likely universities such as Edinburgh and St Andrews, which are popular with RUK students, will have benefited from the introduction of fees.
Robin Parker, president of NUS Scotland, said the body had repeatedly warned of the dangers of introducing a market in higher education into Scotland.
He said: "There's now some evidence that we were right to oppose it and clearly some universities aren't benefiting as much as they thought they would from higher fees, while others could well be benefiting greatly.
"Hopefully this will serve as a timely reminder to politicians of all parties that higher fees and the introduction of a market in education isn't the way to go."
But a spokeswoman for Universities Scotland, which represents university principals, said the sector remained attractive to students form across the UK, with applications buoyant.
She said: "The introduction of fees of up to £9000 for rest of UK students came with uncertainties about what the pattern of demand in the first year of the new scheme would be and there may be further volatility in the coming years."
"The few institutions that have witnessed a drop in demand from RUK students in the first year hope to recover these numbers over the long-term and will have no doubt worked hard to market their unique offering to students over the current recruitment cycle."
The figures also highlighted significant differences in bursary payments paid to RUK students by Scottish universities.
Across Scotland, universities are spending an average of 15% of their fee income on bursaries to ensure they do not become havens for rich students.
However, universities are spending very different amounts on bursaries with Heriot-Watt, in Edinburgh, investing 37% of its fee income on student support compared to lower contributions from institutions such as Stirling, Robert Gordon, in Aberdeen, and Strathclyde, in Glasgow.
Mr Parker said: "It's encouraging to see many providing a good proportion of fee income for the poorest students, but this good average is being pulled down by those offering little support."
Universities Scotland said: "Scotland's universities are offering a package of means-tested bursaries that slightly betters that available from universities in England, despite the absence of a regulator."