"(The Transportation Security Administration) has immediately begun the process of paying its workforce. TSA officers should begin seeing paycheques as early as Monday," DHS said on Friday.
President Donald Trump on Thursday said he would take executive action to pay TSA workers and issued a memo directing the payments for Friday.
The TSA earlier on Friday said nearly 12 per cent of airport security officers did not show up for work on Thursday, the most absences since mid-February.
Major disruptions, including airport security lines of several hours or more, were reported at a number of major airports on Thursday and again on Friday.
The TSA said more than 3450 officers did not show up for work on Thursday, including more than one-third of officers at New York's JFK and at airports in Baltimore, Houston and Atlanta.
The TSA cited reports of lines of four hours or more at airports across the country, the worst lines in the agency's nearly 25-year history.
Airline officials told Reuters that absences and lines could worsen this weekend if there were no concrete details on how TSA officers would be paid. Nearly 500 airport security officers have quit since February.
It is unclear how long the funding will last or whether Trump would tap funding for the Homeland Security Department approved in 2025 as part of a massive tax and spending bill.
Democrats in Congress have held up funding for DHS while demanding a change in rules governing its immigration operations, after agents in Minneapolis shot and killed US citizens Renee Good and Alex Pretti.
Republican leaders in the US House of Representatives on Friday rejected a bipartisan Senate compromise to end the six-week deadlock over DHS funding.
Congressional Democrats had proposed funding TSA separately while negotiating over reforms on how Immigration and Customs Enforcement agents operate.
The TSA had reiterated on Wednesday that the agency could be forced to close smaller airports if staffing issues worsened.
Airports are grappling with a school spring-break travel surge with about five per cent higher volume than 2025.
Hundreds of US immigration agents and Homeland Security Investigations officers began deploying at 14 US airports on Monday to aid security screening.
