They also damaged five cars parked in one of the buildings on the site at Kesh Road, Irvinestown. Several of the vehicles had windows broken and wheels removed.
Police say the vacant factory was entered sometime between Wednesday, December 19, and Friday, December 28.
They are keen to hear from anyone who saw vehicles entering or leaving the premises over the Christmas holiday period.
The number to call is 0845 600 8000, quoting reference number 456 28/12/12.