The Senate voted 54-41 Friday to confirm Alejandro Mayorkas as deputy secretary of Homeland Security.

Some Republicans criticized the nomination of Mayorkas because he is being investigated on allegations that he abused his position as director of the U.S. Citizenship and Immigration Services.

“There is still an ongoing investigation,” Sen. Tom CoburnThomas (Tom) Allen CoburnMr. President, let markets help save Medicare Pension insolvency crisis only grows as Congress sits on its hands Paul Ryan should realize that federal earmarks are the currency of cronyism MORE (R-Okla.) said Friday. “Never before has the Senate confirmed someone in this high of a position who is under investigation. ... We should wait for this investigation to be completed.”

Sen. Patrick Leahy (D-Vt.) said the allegations were “lies and smears” motivated by politics.

“I was obvious this was done for political motives not to make Homeland Security a better department,” Leahy said.

Coburn said he took “great offense” to Leahy’s characterization of the situation.

Earlier this week, the Senate voted 78-16 to confirm Jeh Johnson as the new secretary of Homeland Security.

Friday's vote came after Senate Majority Leader Harry ReidHarry Mason ReidMcConnell not yet ready to change rules for Trump nominees The Hill's Morning Report — Sponsored by CVS Health — Trump’s love-hate relationship with the Senate Trump to press GOP on changing Senate rules MORE (D-Nev.) announced an agreement to confirm just three of President Obama’s nominees before the holiday break, rather than the 10 that Democrats had sought.

Republicans have been forcing the use of all debate time on legislation and other nominations to protest recent changes that Democrats made to filibuster rules.

Last month, Democrats unilaterally voted to change the filibuster to allow some executive and judicial nominees to advance on a simple majority vote.

Earlier this week, Reid filed cloture on 10 Obama nominees. He threatened to keep the Senate in session through Christmas Eve in order to complete work on the nominations, but Thursday night a deal was reached avoiding that scenario.

Under the agreement, the Senate will resume work in January on the nomination of Janet Yellen to lead the Federal Reserve.