COSLA calculates that the implementation costs over the first five years could be as much as£500m, more than double the figure mentioned in the report.
Commenting following publication of the report Mr McCafferty said: 'Councils are responsible for paying teachers, so it is vital for us that the recommendations are accurately costed.
'According to our initial calculations, the report has underestimated some aspects and failed altogether to cost others.
'At this stage the key point is to make sure we know exactly what it is that we need to take education forward, and that we have the means to deliver on whatever is collectively decided.
'There appears to be much to welcome in Professor McCrone's report. I hope it will be an important building block towards a better education system in Scotland.
Mr McCafferty continued: 'There must be no hidden agendas and no hidden surprises, the education system in Scotland and our young people must be the winners here.'
He concluded: 'We have already started to examine the implications of the report and we will have more to say over the coming weeks. We also look forward to a positive and constructive dialogue with the trade unions and the government to see how the report can be taken forward in a manner that is acceptable to all.
COSLA President Norman Murray, added: 'A lot of interest in Professor McCrone's report will focus on the cost involved in implementing its recommendations. But excellence does not come cheap. Our children and young people are our future and we cannot afford to skimp on the quality of education we provide for them.
'Recognising and rewarding excellence is vital if we are to achieve one of our other goals which is to raise standards. If McCrone's recommendations help to achieve that they will be well worth it. That is why we will be viewing them as part of a long term investment for the good of Scottish education.'
Mr Murray concluded: 'We have made it abundantly clear to ministers that local government budgets are already fully stretched and that the Government will have to meet its full share of the bill. So COSLA's message could not be starker. If McCrone's recommendations are not funded centrally, then they cannot be implemented.'