Ofsted found fewer pupils taking meals in about 70% of the 27 schools visited since healthy eating rules came in.
It called on schools to work to eliminate the factors discouraging pupils from having school meals.
New guidelines announced in March 2005 limited the amount of processed meats, deep fried and high fat foods served.
They also required schools to provide more fresh fruit and vegetables.
The changes were prompted by TV chef Jamie Oliver's campaign.
But successive surveys by organisations including the School Food Trust, the body appointed to oversee the changes, have suggested take-up fell as a result.
Fewer meals were served in 19 of the 27 schools Ofsted visited, with reductions ranging from 9% to 25%.
Ofsted said the reason for the decline was "complex" and included a lack of consultation about the new arrangements with pupils and parents and poor marketing of the new menus.
