The curriculum was simply not suited to the small numbers who become disaffected and account for a large percentage of absences, Mr Aitken said.
By S4, the truancy rate rises to 2 per cent. "We have to develop an alternative curriculum, more vocationally oriented, to rekindle young people's motivation and enthusiasm," he said.
Mr Aitken, Edinburgh's education spokesman, admitted Scottish Executive figures make "grim and sad reading" but insisted it was a very small minority who caused the difficulties.
"Reasons for staying away from school are wide-ranging and complex. They can involve peer pressure and bullying, disaffection, caring responsibilities at home, and abuse and neglect, all of which need individual responses," Mr Aitken said.
"And there is no hiding the fact that schools in neighbourhoods with high levels of deprivation face commensurately higher levels of absence."
Mr Aitken said it was important to keep statistics in perspective and understand the issues behind truancy. The vast majority of pupils attended school for more than 90 per cent of the time.
The Executive's figures show that 2 per cent of truants account for half of absences and 10 per cent account for 90 per cent of all truancy. About 143,000 pupils, or 20 per cent, were recorded as truanting at least once during 2004-05.
Peter Peacock, Education Minister, said the figures were still too high.
"We know a small percentage of pupils account for most truancy but too many are trying it for the first time. That is why we are backing schools with new investment to use automated call systems," Mr Peacock said.
Evidence from pilot schools showed that secondaries could halve their truancy rate by using call systems to contact parents or carers immediately if children fail to show at school.
The official statistics confirm Mr Aitken's analysis of disaffection among the disadvantaged, especially in the secondary sector. Schools with higher levels of deprivation have higher levels of absence, but the Executive cautions that "there are many schools which did not follow this trend".
Pupils - particularly boys - on free meals were off for an average of 10 days more and those with a record of need or individualised education programme were off for an average of four days more. "Of these, pupils with social, emotional and behavioural difficulties have the highest rate of absence," the Executive notes.
In another key category, looked-after children were absent on average 10 days more, with those looked after at home missing an average of six weeks'
The Executive states: "Where a child has multiple risk factors (is registered for free meals, has a record of needs and is looked after), they are on average absent for just over six weeks."
In its public comments, the Executive confirms that sickness is the main reason pupils are not at school, and as a factor is more than three times higher than truancy. For every 28 days lost to sickness, eight are lost due to truancy and five for being on holiday during term time.
Mr Peacock reminded parents of the need to "think very carefully indeed about whether that is absolutely necessary".
The Executive study also confirms that levels of sickness rise sharply among girls in secondary. Deprivation is yet again another factor in the statistics.
Mr Peacock stressed that more will be done to prevent truancy as automated call systems expand with Executive backing. So far, 319 schools are involved - one special school, 141 primaries and 177 secondaries.