The review's findings, which have just been made public, also state that some school registers had marked pupils as present when they were absent.
It highlighted that absences were being authorised without "sufficiently rigorous checking", leading to "artificially low levels of unauthorised absence".
This made it impossible for the council's education welfare service to act.
A report by chief education officer Mick Waters containing the audit's results said unauthorised absence remained a priority for both his local authority and the Government.
But the emphasis on improving this rate "offered a perverse incentive to schools to authorise absence too freely". Some schools in Manchester now had authorised absence rates of 10 per cent or more, he added.
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