(CNN) -- Airline passengers may be asking themselves: Are those longer lines at airports due to federal spending cuts?
The answer is yes and no.
If you are at a Transportation Security Administration (TSA) checkpoint, relax. You're just experiencing a normal wait. Agency cuts have not yet taken effect, but stick around.
TSA says you'll be experiencing longer wait times in coming weeks and months -- the result of furloughs, overtime cuts and a hiring freeze.
But if you're on the customs line at New York's John F. Kennedy airport, Miami International or a few others, you, indeed, are feeling the first impacts of the spending cuts on the aviation system.
JFK airport had approximately 56 flights with wait times in the arrival area of customs exceeding two hours and 14 flights experiencing related waits of more than three hours, according to Jenny Burke, a spokeswoman for Customs and Border Patrol.
Miami had 51 flights reporting waits at customs exceeding two hours and four flights approaching or topping three hours.
"These wait times are not typical for this time period and are related to decreased booth staffing," Burke wrote to CNN.
Cuts in overtime forced the customs agency to close several booths and the situation will worsen after furlough notices go out on March 7, she said.
More than $85 billion in automatic, government-wide spending cuts took effect on Friday night. The Obama administration said the so-called sequester would hit air travel, particularly hard, through cuts in spending on air traffic control and security.
Homeland Security Secretary Janet Napolitano said on Monday the airport lines this weekend were just the tip of the iceberg.
"We will see these effects cascade over the next week," she said.
"I don't mean to scare, I mean to inform. If you're traveling, get to the airport earlier than you otherwise would. There's only so much we can do with personnel," Napolitano said. "And please, don't yell at the customs officers or the TSA officers. They're not responsible for sequester."
Napolitano said she expects wait times to double in some cases, if the cuts continue for the next several months.
"There's very little we can do to mitigate it because the procedures we use to clear passengers and cargo, they're responsible I think for the fact that we have a very safe aviation system and we have a very good land migration system where we know who's coming into the country," she said.
"So, we're not going to cut back on those security needs so the end result is fewer people doing the same thing means lines are going to get longer."
The TSA said a hiring freeze will take effect in April. That will result in an additional 1,000 screener vacancies by Memorial Day weekend and up to 2,600 vacancies by September 30, the end of the fiscal year. The TSA has approximately 50,000 screeners.
"With TSA staffing levels decreasing over time, we expect that during busy travel periods wait times exceeding 30-40 minutes could double at nearly all of the largest airports," the TSA said in a statement.
"In addition, passengers who schedule their travel outside of peak flight schedules and plan to arrive close to their scheduled flight time may see their wait times reach 30 minutes or more," the TSA said.
The Federal Aviation Administration said on Monday that there were "no immediate impacts" from spending cuts. But it has predicted flight delays when it begins furloughs -- one third of whom are air traffic controllers.