The Senate voted 60-40 Wednesday, narrowly ending debate on the controversial nomination of Tom Perez to be secretary of Labor.

Republicans agreed to hold an up-or-down vote on his nomination as part of a deal to avoid Senate rule changes limiting the minority's right to filibuster executive branch nominees.

The close vote — 60 votes were needed to move the nomination forward — came after several GOP senators complained that Perez has engaged in “ethically questionable” actions while heading the Civil Rights division of the Department of Justice.

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“We have a Department of Labor nominee that has a record of ideological, polarizing leadership,” Sen. John CornynJohn CornynMcConnell names Senate GOP tax conferees Air Force makes criminal reporting changes after Texas massacre We need a better pathway for allowing civilians to move guns across state lines MORE (R-Texas) said ahead of the vote. “I believe Mr. Perez’s record disqualifies him from running this or any other federal agency.”

GOP Sens. Lamar AlexanderAndrew (Lamar) Lamar AlexanderOvernight Finance: Trump says shutdown 'could happen' | Ryan, conservatives inch closer to spending deal | Senate approves motion to go to tax conference | Ryan promises 'entitlement reform' in 2018 Senate approves motion to go to tax conference House conservatives, Ryan inch closer toward spending deal MORE (Tenn.), Susan CollinsSusan Margaret CollinsOvernight Health Care: 3.6M signed up for ObamaCare in first month | Ryan pledges 'entitlement reform' next year | Dems push for more money to fight opioids Study: ObamaCare bills backed by Collins would lower premiums Right scrambles GOP budget strategy MORE (Maine), Bob CorkerRobert (Bob) Phillips CorkerFormer Dem Tenn. gov to launch Senate bid: report McConnell 'almost certain' GOP will pass tax reform Former New Mexico gov: Trump's foreign policy is getting 'criticized by everybody' MORE (Tenn.), Mark KirkMark KirkHigh stakes as Trump heads to Hill Five things to watch for at Trump-Senate GOP meeting Giffords, Scalise highlight party differences on guns MORE (Ill.), John McCainJohn Sidney McCainGOP strategist donates to Alabama Democrat Meghan McCain knocks Bannon: 'Who the hell are you' to criticize Romney? Dems demand Tillerson end State hiring freeze, consult with Congress MORE (Ariz.) and Lisa MurkowskiLisa Ann MurkowskiMcConnell names Senate GOP tax conferees Week ahead: Trump expected to shrink two national monuments GOP on verge of opening Arctic refuge to drilling MORE (Alaska) voted with Democrats to advance Perez in his nomination process. There will be 30 hours of debate before a final vote on Perez's nomination unless time is yielded back, meaning the vote could happen as early as Thursday evening.

Sen. Marco RubioMarco Antonio RubioRyan pledges 'entitlement reform' in 2018 Richard Gere welcomes lawmakers' words of support for Tibet Dem lawmaker gives McConnell's tax reform op-ed a failing grade MORE (R-Fla.) urged his Republican colleagues to ignore the deal made to allow up-or-down votes on several of Obama’s executive branch nominees.

“This is the Labor department,” Rubio shouted on the Senate floor. “I am shocked that there are members of my own conference that are willing to go forward on this nominee.”

Rubio said Perez failed to answer lawmakers’ questions during his confirmation hearing.

“We’re being asked to vote to invoke cloture on the nomination of someone who has open contempt to a congressional subpoena,” Rubio said. “This is wrong. How can we possibly — I don’t care what deal was cut — how can we move forward on someone who hasn’t provided information asked for by a congressional committee?”

Sen. Tom HarkinTom HarkinDemocrats are all talk when it comes to DC statehood The Hill's 12:30 Report Distance education: Tumultuous today and yesterday MORE (D-Iowa) said Rubio’s claim that Perez is violating a congressional subpoena is “just plain wrong.” Harkin said Perez submitted the 35 emails in question to the Senate Health, Education, Labor and Pensions Committee and that the Department of Justice now has the emails from his personal account on file.

Sen. Ben CardinBenjamin (Ben) Louis CardinDems demand Tillerson end State hiring freeze, consult with Congress Former New Mexico gov: Trump's foreign policy is getting 'criticized by everybody' Dems put hold on McFarland nomination over contradictory testimony: report MORE (D-Md.) defended Perez’s history of public service.

“Tom Perez has a long history of public service,” Cardin said. “He is a good person who is in public service for the right reasons. … As secretary of Labor, he will use that position to provide the balance we need in our commercial communities … so everyone can benefit from our great economy.”

Republicans have accused Perez of intervening in two court cases for his own "political agenda."