WASHINGTON—President Trump directed federal officials to pay Transportation Security Administration workers, bypassing a gridlocked Congress after the latest proposal to fund the broader Department of Homeland Security ran aground Friday.

The move, which Trump had previewed a day earlier, came as House Republican leaders rejected a Senate-passed bill that would fund most of DHS, including the TSA. A standoff in Congress over immigration enforcement and funding has led to missed paychecks for airport-security workers and long lines for travelers.

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