The U.S. Coast Guard will reduce its patrols off the coast of New York City by 24 percent once cuts due to the sequestration go into effect, Department of Homeland Security secretary Janet Napolitano said Tuesday.

At a security conference in NYPD headquarters, Napolitano said she expected a 50 percent increase in wait times at Kennedy Airport because of the cuts, with some waits in peak periods expected to hit four hours. The longer lines will be caused by airport security staff furloughs and reduced overtime, she said.

Napolitano wasn't specific about which Coast Guard activities would be cut off New York harbor and Homeland Security officials in Washington didn't return a request for comment about her remarks. Three Coast Guard sectors cover the waters off New York City and Long Island, so the pullback in maritime operations could affect them all.

Speaking at a security conference, Napolitano said her agency is working out how sequestration will be impacting the city's major counterterrorism programs, some of which rely heavily on federal funding.

"Sequestration will require reduced funding for various [NYPD] grant programs," said Napolitano, referring to city programs like the lower Manhattan and midtown security initiatives, as well as the use of radiation detectors which are largely funded with federal dollars.

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Napolitano didn't have specifics on the possible impact of reduced funding on those programs, which NYPD Commissioner Ray Kelly has often said are essential to helping shield the city against terrorism.

Congressional officials last week said New York City received $151 million in fiscal 2012, which began in October 2011, in funding from the Urban Areas Security Initiative to help the city plan, equip and train against terrorism.

While the fiscal 2012 funding isn't expected to be affected, the status of a similar Homeland Security request for fiscal 2013 might be affected by the sequestration, officials said.

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The city also gets about $20 million in Securing the Cities money used to purchase radiation detectors and other equipment, which finds its way to Nassau and Suffolk Counties.