The Scottish Executive said the drop in the take-up of lunches in primary and secondary schools, by more than two percentage points to 46.7 per cent followed the introduction of its Hungry for Success healthy eating initiative.
But David Melvin, deputy director of direct and care services at Glasgow City Council, said figures relied on instructions to headteachers to count the number of pupils at one 40-minute sitting.
He said the council's own research had shown that 65 per cent of secondary school pupils were eating school meals, compared to 43 per cent recorded in government statistics.
A spokeswoman for the Executive said it accepted the figures were "just a snapshot" of the situation.