The criticism has emerged in the initial findings of Rachel de Souza's forthcoming review of school attendance rates, which is due to be published later this year.
She requested attendance data from all 151 councils in England for her review.
But while almost all responded, only around half were able to handover estimates of persistently absent children.
Data supplied by councils suggests that more than a fifth of pupils who missed lessons are persistently absent and 1.5 per cent are severely absent.
“Despite being a country that collects more data than most on school attendance, the system has significant weaknesses in supplying accurate, and in some cases, credible numbers on those children who are losing out by either not being in school at all, or who are persistently or severely absent from school they are enrolled at,” said de Souza.
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