The findings from the Project on Assessment in Scotland-using Information Technology (PASS-IT), an initiative backed by the Scottish Executive, show that "changing the medium" has little effect in chemistry or computing.
In maths, the picture was more complex with "weak evidence" of differences between paper and computer-based tests, at both Higher and Advanced Higher.
These are interim findings based on phase one of research into the three subjects, involving more than 400 candidates.
Many of the issues surrounding online assessment are, inevitably, technical: in maths, for example, partial credit can be awarded for performance on paper while an ICT-based exam makes optional steps available to the student (but where a penalty of lost marks can be imposed for choosing steps).
All the data from the project is subject to further analysis before more watertight conclusions can be drawn and a final report will be issued towards the end of the year. Further work will cover Intermediate English, Higher French, Higher music and Access and Intermediate maths.
Alan Irons, the project co-ordinator, believes it is at the leading edge of e-assessment research and has significant implications for students and teachers.
Focus groups have highlighted diverse views among teachers and lecturers, according to Jim Rand, who carried out an internal evaluation. This ranged from "those who were extremely positive and enthusiastic to those who were concerned and sceptical".
Mr Rand suggested that teachers' continuing professional development should be used to extend their awareness of the issues.
Despite the growing interest in online assessment, the Scottish Qualifications Authority has been urging caution. "A great deal of research still has to be done in order to make such a system deliverable and flexible," Anton Colella, its chief executive, says.
Martyn Ware, the SQA's business manager, believes the authority is right to be "cautious but engaged".
But Mr Ware suggests that the evidence emerging from the PASS-IT project so far is positive. He told The TES Scotland: "Experience with online assessment is demonstrating a number of very positive findings. The systems don't fall over every time you use them. They are secure. Candidates often quite like to do assessments online. Teachers and centre staff can understand and work with the software."
Christine Bond, a maths teacher at Balerno High in Edinburgh, which has been testing online assessment, says there have been access problems but reduced teacher workload has been a major bonus. "I'd like to see all end-of-unit assessments online as soon as possible. Pupils would soon get used to it."