The company says that the current "challenging" economic climate could mean 44 jobs go at Great Witchingham in Norfolk and Holton in Suffolk.
The job losses will be from "salaried staff and hourly paid engineers" according to the company.
In a statement a company spokesman said: "As a company we are constantly looking at ways of making the business better able to cope with the challenging and highly competitive economic environment and these structural changes are part of this process.
"Our priority is to make Bernard Matthews as efficient as possible to ensure a sustainable future for the whole workforce.
"We will be entering into consultation with affected staff, which may cause a degree of uncertainty for these individuals. To minimise this it is our intention to provide regular information updates throughout the process."
The two plants employ 2,200 people.