Cities Are Flouting Flood Rules. The Cost: $1 Billion.

Other places have faced no consequences. In many cases, local officials reported having never even been told by FEMA that they were doing something wrong.

In Chesapeake, Va., which, according to FEMA’s data, has 650 structures built below the flood level, permit director Jay Tate said he didn’t know which homes were in violation of the rules. He said the city joined the program in the late 1970s, but didn’t start enforcing the rules for perhaps a decade or more. “It probably wasn’t until about 1990 that we had a robust review of building plans to make sure it was in accordance with that,” Mr. Tate said.

In nearby Poquoson, Va., which FEMA shows as having 469 homes that fail to meet its provisions, about 10 percent of all homes in the city, floodplain manager Ken Somerset said the agency hadn’t alerted him to the issue. “I would be interested to see that list,” Mr. Somerset said.

In Pinellas County, Fla., which has almost 4,000 structures that are too low, floodplain manager Lisa Foster said there were different possible explanations, including inaccurate elevation measurements. She said the county would have no way of knowing how many structures were built in violation of the rules “without doing a detailed analysis of the data for each,” and said she wasn’t aware of FEMA contacting the county about the problem.

“Pinellas County has a very active floodplain management program,” Ms. Foster said in a statement.

In the Florida Keys, Christine Hurley, assistant administrator for Monroe County, likewise said she had no knowledge of FEMA warning officials about the county’s more than 3,000 structures that are too low.

One of the counties with the greatest number of affected properties in the country is Cape May, N. J., where FEMA data says 3,308 structures are too low. When asked about the figures, Martin Pagliughi, the county’s emergency management director, said he had never heard the term “minus-rated” that FEMA uses to describe structures that are too low.