MANKATO — The Federal Emergency Management Agency is asking Mankato and North Mankato to pay for a study to ensure the levee system is still working — something that could cost the cities hundreds of thousands of dollars even as they are struggling to cut budgets in response to the deep recession.

FEMA is updating its nationwide flood insurance rate maps, which are widely used to calculate risk and liability for floods. To make new maps, FEMA is requiring levee owners to show their flood-protection systems still work.

“There are levees across this nation that are very old and FEMA realized that they can’t show that a levee protects against flooding unless it can be certified,” FEMA spokeswoman Laurie Smith-Kuypers said.

The certification standard remains protection against a 100-year flood, also stated as the flood that has a 1 percent chance of occurring in a given year.

A Twin Cities engineering firm gave North Mankato Emergency Management Director Marion Hayer a “very rough ballpark estimate” that the certification could run from $50,000 to $100,000 per mile of levee. In the case of North Mankato, which has 2.4 miles of levee, that would mean $120,000 to $240,000.

Mankato Public Works Director Mark Knoff said federal regulations say a levee’s owner — the cities, in this case — are responsible for such studies.

In the past, the cities turned to the U.S. Army Corps of Engineers for such work, typically at little local cost.

But in 2000, the last time Mankato’s rate map was updated, a little-noticed amendment was added to a federal water bill by Sen. Craig Thomas, a Wyoming Republican, requiring cities and other governments, whenever possible, to turn to the private sector rather than Corps of Engineers to provide services such as the levee recertification. The amendment was prompted by concern that the Corps was competing with private engineering firms.

Mankato officials are weighing their options, but the North Mankato City Council struck a more acerbic tone at Tuesday night’s meeting.

“We need to be going to (Congressman Tim) Walz and (Sen. Amy) Klobuchar and all the others and begin screaming,” said North Mankato Councilwoman Diane Norland.

North Mankato Mayor Gary Zellmer said he couldn’t believe the FEMA letter, which he received last month. The letter gives the cities just 90 days to sign the agreement obligating them to the recertification and the unknown costs of doing the study, which must be completed within two years.

“I’m reading it and thinking ‘What the H is this?’,” Zellmer said.

The council voted unanimously to contact Mankato and possibly other cities in the state in an attempt to get emergency congressional action.

“Realistically, we’re not going to be able to do this,” Zellmer said of the expenditure. “We don’t have $120,000 or $240,000.”

If the cities don’t do it, however, maps could be redrawn labeling lower-lying areas of the cities as high-risk of flooding, said North Mankato City Engineer Brian Malm. And that change would force home-buyers to purchase expensive flood insurance to obtain a mortgage.

FEMA’s Flood Map Modernization program is the first time the agency has systemically sought out certifications for levees. There’s no length of time certified by law that says how long such a certification might last, said Ken Hinterlong, branch chief for risk analysis in FEMA’s Chicago office.

Mankato City Engineer Ken Saffert said the city and the U.S. Army Corps of Engineers already inspect the levee every year.