In her annual report, Susan Lewis also said few schools were following new guidance from the Assembly government on combating non-attendance.
Ms Lewis calculated that enough pupils were absent from Welsh secondaries in 2004-5 to fill 20 average-sized schools. And she predicted an Assembly government target to cut rates in secondary schools to below 7 per cent by this autumn would not be met.
Latest figures in the report show there were an average of 20,000 pupils absent from secondaries in 2004-5. Ms Lewis said schools had to create an ethos where it was the norm for pupils to work hard and attend regularly to see rates drop.
She said this meant changing attitudes, with more links with families and the wider community. Elsewhere in her report, she said unruly pupils should be referred to behaviour support services before exclusion - not after.
Figures in the report show that exclusions have risen from 16,530 in 2003-4 to 20,242 in 2004-5.
Early intervention has long been touted as a way to stop children going off the rails. Pupils can be badly behaved for a variety of reasons, including traumatic events at home. However, many heads say referral is often a laborious process, with staff shortages of case workers employed with local education authorities.
Ms Lewis also found disruptive behaviour was still a major issue for 70 per cent of schools. But, in a similar view to last year, she said unruly children were still in the minority. During the year, Estyn found behaviour was at least good with outstanding features in 41 per cent of primary schools, but only 27 per cent in secondaries.
Examples of disruptive behaviour cited in the report were over-chatty pupils, cheek, avoiding work or disrupting the work of other pupils.
The schools that were most successful in managing bad behaviour made sure staff, pupils and parents were clear about the rules, rewards and sanctions.