AQA, the largest board for GCSEs and A-levels, said it would not allow GCSE English to be marked on screen because of concerns over the difficulty of making annotations to scripts.
But Edexcel, AQA's rival, is pushing ahead with marking millions of papers on screen, despite the concerns of some examiners.
Last autumn, Edexcel faced controversy after a handful of teachers told the BBC of their frustration at having marked scripts returned without comments or annotations.
Traditionally, markers have written comments, ticks and crosses as they grade scripts on paper. These can then be seen if a school wants to challenge a result.
But the introduction in the past five years of online marking, in which scripts are scanned and then marked at the computer screen, appears to have changed this process.
Edexcel says its system does allow examiners to annotate using a technical tool. But critics say they are not using it, so even A-level scripts can come back without annotation.
Speaking at the Chartered Institute of Educational Assessors conference in London this week, Michelle Meadows, AQA's principal research manager, said: "The problem we are really struggling to overcome with the software we have at the moment is allowing annotations. We do have a tool that allows you to make annotations on scripts, but there are issues about the fact that ... using it might interrupt an examiner's thinking.
"That's why we are going to be a bit cautious in extending this technology, especially in subjects such as GCSE English."
The board is also concerned that marking essays on screen could cause eye strain.
On-screen marking is seen as a key element of the modernisation of the exams process, and Dr Meadows said AQA was committed to extending it in the long term.
She said it had advantages, including automating the totalling of marks and keeping a real-time track on the quality of examiners' work.
Last year, AQA marked 1.7 million of its GCSE and A-level scripts on-screen, compared to 3.9 million at Edexcel. The OCR board is also cautious about expanding the use of the new technology.