It says there is a culture of "fundraising, reward and celebration" that frequently involves foods that are high in salt, sugar and fat.
In one case, a secondary school told forms it would get doughnuts if they had 100% attendance for a month, while in another, a teacher said pupils were offered pizza and fried chicken as encouragement to take part in weekend revision sessions.
The study, led by the Jamie Oliver Food Foundation, in partnership with others including Sheffield University, is based on interviews and surveys of pupils, parents and teachers as well as school visits.
It found that just over half (53%) of secondary teachers polled, along with a quarter (26%) of those working in primaries, said their school rewards include foods that are high in salt, fat and sugar.
"In one secondary school they told us that whole forms would be rewarded with doughnuts if they achieved 100% attendance in a month," the study says.
"School staff are aware that their reward and celebration practices contradict healthy eating practices," it adds, quoting one as saying: "We've been known to provide KFC/Domino's Pizza as an incentive for weekend revision sessions, obviously seen as a treat but cannot do the children's attitude towards food any favours."
The findings also show that 86% of secondary teachers and 85% of those in primaries say their school fundraising activities include cake and bake sales.
In addition, 68% of secondary and 58% of primary teachers said their school celebrations involve these types of sweet treats.
"The culture of high fat and sugary foods used as rewards, in fundraising and in celebrations, is creating social and physical environments that contradict children's food education," the report says.
"This appears to be recognised by pupils and school staff, and there is an appetite from parents for the use of such foods in this way to be limited to once a term."