The incident happened about 1.45pm at a Douro Street graphic supplies company.
The four-metre long sheets tipped onto the two men while they were loading them onto pallets, resulting in the workers being trapped for nearly an hour.
The men, one aged in his early 20s and the other in his late 30s, who are employed by a labour hire company, were airlifted to the Alfred Hospital with serious injuries. WorkSafe is at the scene investigating the cause of the incident.
WorkSafe has issued a prohibition notice, immediately suspending operation until a safe system of work has been established.
Incidents where workers have been crushed by materials shifting while inside shipping containers are a common problem and workplaces need to ensure safe systems of work are in place to prevent incidents like this.