The present invention discloses a method and apparatus for sterilizing containers with gas-phase hydrogen peroxide and heat on a linear form, fill and seal packaging machine. A partially formed container is subjected to multiple applications of gaseous hydrogen peroxide and hot air within a sterilization tunnel. The sterilization tunnel is maintained at a temperature greater than the condensation temperature of hydrogen peroxide. The present invention sterilizes the container allowing for filling of the container with a high acid product such as orange juice for ambient distribution. The container may be any number of possibilities such as TETRA REX.RTM. gable top cartons, plastic bottles, and the like. The invention allows for the efficacious use of hydrogen peroxide gas having a concentration of up to 53%.