ATLANTA -- Kellogg Co. has blamed a nationwide shortage of Eggo frozen waffles on heavy rain that shut down one of its main plants in Atlanta. But that's only part of the story.

The Atlanta facility was closed during much of September and October to sanitize the plant after inspectors found Listeria monocytogenes -- bacteria that can cause serious infection -- in a sample of Eggos, according to the Georgia Department of Agriculture. An ABCNews.com reader raised the issue in a comment posted on an earlier story.

Kellogg agreed to recall about 4,500 cases of Eggos Sept. 2 after a routine state inspection turned up Listeria in a sample of Buttermilk Eggo Waffles. The Centers for Disease Control and Prevention considers Listeria harmless for most people but it can be particularly dangerous for pregnant women, newborns and people with weakened immune systems.

"Kellogg voluntarily ceased production at the plant, began an investigation to determine a possible cause of contamination and began a regimen of cleaning and sanitizing," the Georgia Department of Agriculture announced at the time. "Kellogg will execute its hygienic restoration plan under GDA before it resumes production at the plant."

Kellogg spokeswoman Kris Charles said the plant was closed for both cleaning and as a result of the flooding.

"Just as the Atlanta facility was ready to resume production, excessive rain in the region caused flooding at the facility, which delayed the startup," Charles wrote in an e-mail to ABC News Wednesday.

Left unanswered were questions about how long the plant was closed for flooding and how long for cleaning bacteria.

Oscar Garrison, assistant commissioner of consumer protection at the Georgia Department of Health, told ABC News Wednesday that Kellogg had entered into an agreement with state and federal officials on a "hygienic restoration plan" that took several weeks. In late September, as Kellogg was ready to reopen the plant, heavy rains hit Atlanta.

Flood water filled the Eggo plant parking lot, Garrison said, but did not appear to enter the plant. Still, he said, "Kellogg wanted time to do their hygienic restoration over again.

"They wanted to be real comfortable that they got every potential source of Listeria," Garrison said. "They wanted to do a thorough evaluation."

So, Kellogg launched the cleanup operation again -- scouring the plant, hiring private inspectors to review everything and then letting state and federal investigators back in to give a final sign-off before reopening. The Eggo plant remained closed until late October. It's now back up and running.

Charles said earlier this week that the heavy rains were to blame for knocking out Kellogg's waffle operations in Atlanta.

"We are experiencing temporary Eggo supply constraints caused by a confluence of events," Charles wrote. "Flooding at our Atlanta facility as well as equipment issues necessitating extensive enhancements and repairs at our largest waffle bakery facility."

There was no mention of Listeria, nor is it mentioned in an "FAQ" about the shortage posted on the Eggo Web site. Garrison confirmed that flooding delayed the reopening of the plant, although it's not the reason it was closed.

"I really believe if the flooding had not happened," Garrison said, "They would have been ready to open [in late September]. But they really wanted to take that extra precaution."

Some shoppers searching for Eggos have found empty freezer shelves and apologetic signs. At the top of the Kellogg's Web site is the message: "Some of your favorite Eggo products are out of stock nationally. We are working hard to fix this short-term issue." Kellogg said shortages could last until the middle of next year.

"We are working around the clock to restore Eggo store inventories to normal levels as quickly as possible," Charles wrote. "In the meantime, we're allocating available product to customers based on historical percentage of business. We estimate that store freezer inventory shortfalls will continue on Eggo products through the first half of 2010."