Monitoring of the catering contracts under CCT found that up to £12,000 worth of meals were unaccounted for at a dozen schools.
A council spokesman said that in future meals would have to be paid for either by the school or the teacher.
But Liverpool Association of Secondary Headteachers chairman Alan Smithies told the Post: 'It is the principle of the thing. What has been a custom is disappearing. The teachers are working for that hour, they don't get payment and even the canteen staff recognise it is a good investment and it helps to keep the pupils in order'.