The company's Atlanta plant was shut down for an undisclosed period by a September storm that dumped historic amounts of rain in the area.
Meanwhile, several production lines at its largest bakery in Rossville, Tenn. are closed indefinitely for repairs.
Company spokeswoman Kris Charles says it will take until the middle of 2010 before shelves around the country are stocked at pre-shutdown levels.
Already customers are noticing near-empty Eggo shelves on the freezer aisle at many grocery stores. They are lamenting the shortage on blogs, Twitter and Facebook.
