Airports like JFK and Houston report shorter wait times, though LaGuardia still faces delays of up to two hours.

Following weeks of long lines at United States airport security checkpoints, operations are starting to return to normal after US President Donald Trump signed an emergency directive ordering payment to Transportation Security Administration (TSA) workers last week.

Airport security checkpoints across the country are seeing much shorter lines, including at New York’s John F Kennedy (JFK) International Airport, where wait times are now under a half hour, and at comparable hubs like Houston’s George Bush Intercontinental Airport and Baltimore’s Thurgood Marshall Airport.

While delays are decreasing at many major airports, that’s not the case everywhere. As of 1pm in New York City (17:00 GMT), lines at LaGuardia Airport, which primarily serve destinations in the US, parts of Canada, and the Caribbean, are reaching 90 minutes at Terminal B.

On Friday, US Homeland Security Secretary Markwayne Mullin said TSA workers “should begin seeing paycheques as early as Monday”. Trump’s action came after Republicans in the US House of Representatives rejected a Senate-passed bill to fund most of the Department of Homeland Security (DHS).

TSA agents called out in record numbers over the weekend, with 10.59 percent calling out on Saturday and 12.35 percent on Friday, DHS confirmed. Al Jazeera requested specific call-out numbers for Monday, which the agency did not provide.

Looming paycheques are coming as negotiations in Congress continue to stall amid the partial US government shutdown, which is entering its 45th day.

“At the direction of President Trump and the Secretary of Homeland Security Markwayne Mullin, TSA has immediately begun the process of paying its workforce,” Lauren Bis, a spokesperson for the Department of Homeland Security, said in a statement to Al Jazeera, noting that TSA officers should begin seeing payment “as early as today”.

“TSA officers are grateful to the president and secretary for their leadership to put money back into the pockets of TSA employees who worked without pay during the ongoing Democrat DHS shutdown. Working without pay forced more than 500 officers to leave TSA, and thousands were forced to call out,” Bis said.

While the agency blamed Democrats through official channels, Republicans voted against measures to fund TSA nine times, though House Republicans voted on Friday night to fully fund DHS for 60 days. The bill, which would have included funding for DHS, was “dead on arrival”, according to a statement by Senate Minority Leader Chuck Schumer.

Despite shorter airport lines, US airline stocks continue to drop on Wall Street. United Airlines stock is down 2.4 percent in midday trading, Delta is down 1.5 percent, American is down 0.4 percent, and budget carrier Southwest has tumbled by 1.9 percent.