An interim report from the Assembly government shows that nearly 95 per cent of secondaries in 17 local education authorities use electronic registration software to monitor attendance. No figures are available for the other five Welsh LEAs.
The rate of change is much lower in primaries, with more than a third (36 per cent) retaining old-style paper methods.
The pressure for electronic registers is coming from the Assembly government, which wants to set a minimum standard for the quality of attendance data in schools.
It expects all secondaries to start returning data on pupil absence in mornings and afternoons in 2006-07. The same target is set for primaries for 2007-8, and pound;6 million has been set aside for electronic registers from 2005 to 2008.
An interim report, compiled last term, found individual schools were taking the lead in installing the systems, with some meeting the cost themselves.
Phil Whitcombe, head at Bryn comprehensive in Barry, south Wales, said its new pound;10,000 wireless system would improve pupils' safety and provide accurate, up-to-the minute data. Pupil's movements can be tracked between lessons using a swipe card that identifies any missing pupils, inside or outside the school.
Alwyn Thomas, head at Bridgend's Bryntirion comprehensive, said old-style registration was a "cherished" feature of school life that would be missed.
But he said a new pound;6,000 system using fingerprints, rather than names, to record absence was the way forward for his school.
At present, sixth-formers and visitors enrol in the school using a fingertip signature and photograph using the VeriCool system.
Mr Thomas said it would be extended to all year groups in 2006, adding: "As mentors and business people visit, and more pupils go out to work placements, this system is a fail-proof way of keeping track of everyone."
Primaries feel less need for electronic systems. Only 30-40 primaries reported using them in classrooms. One head said: "I can only see them as a waste of time in primary schools."
The report notes differences in the systems being used. In Monmouthshire, funding has been focused on a complex lesson-by-lesson system in a school with high truancy rates. But Gwynedd is targeting a large number of primary schools with a basic electronic ampm registration system.