An analysis by Dr Connelly shows that Scottish Qualifications Authority results cover only about half of looked-after children because schools often do not identify them.
"In short, without accurate reporting we cannot be clear whether things are improving, remaining static or getting worse," he said.
His comments echo those of the inspectors, who this week underlined the Scottish Executive's concern that many pupils are continuing to miss out on their education.
Young males who by the age of 21 are not in education, employment or training (the NEET group) for six months are three times more likely than the average to suffer mental health problems, five times more likely to have a criminal record and six times less likely to have any qualifications, the HMIE points out in its report, Missing Out.
Graham Donaldson, senior chief inspector, urged a refocusing on the educational difficulties of the lowest-performing 20 per cent of pupils and questioned whether the attainment gap between the lowest and highest performers was measured accurately.
"Are schools and education authorities clear about which of their pupils fall within the lowest-attaining 20 per cent nationally, and which approaches to improving their attainment are most effective?" he asks.
The inspectors emphasise that twice the proportion of pupils who leave school with no qualifications are found in the 15 per cent most deprived areas.
Conflicting evidence about the performance of looked-after children and the lowest attainers emerged this week.
Data on 5-14 attainment in reading, writing and maths, analysed by Dr Connelly, shows continu-ing under-performance among looked-after children (LAC). As an illustration, in P3 in 2003, 74 per cent of such children reached level A in reading against 88 per cent of their peers. In 2004, those figures were 65 per cent and 85 per cent respectively.
In S1 in 2003, 42 per cent of looked-after children reached level D or above in reading compared with 74 per cent of non-LAC. In 2004, the figures were 41 per cent against 76 per cent.
Dr Connelly cautions against reading too much into the apparent drop in performance, given the incomplete data and changing cohorts year to year.
Nevertheless, he says: "In crude terms, what these figures show is that, unsurprisingly, LAC on average perform much less well than non-looked after children."
At the same time, the HMIE contends that results from the international Pisa 2003 study show Scotland is closing the attainment gap when other countries are not. "The performance of the lowest 25 per cent of students in reading literacy has improved and the gap in scores has narrowed to 15 per cent. While this was not statistically significant, no other OECD country had narrowed the gap in scores by as much," say inspectors.
Missing Out: a report on children at risk of missing out on educational opportunities was published yesterday by HMIE.