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 CornynGun proposal picks up GOP support House bill set to reignite debate on warrantless surveillance Republicans jockey for position on immigration 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 AlexanderChildren’s health-care bill faces new obstacles Overnight Health Care: Schumer calls for tying ObamaCare fix to children's health insurance | Puerto Rico's water woes worsen | Dems plead for nursing home residents' right to sue Schumer calls for attaching ObamaCare fix to children's health insurance MORE (Tenn.), Susan CollinsSusan Margaret CollinsGun proposal picks up GOP support Giffords, Scalise highlight party differences on guns Agricultural trade demands investment in MAP and FMD MORE (Maine), Bob CorkerRobert (Bob) Phillips CorkerDeficit hawks voice worry over direction of tax plan The Hill Interview: Budget Chair Black sticks around for now Overnight Finance: White House requests B for disaster relief | Ex-Equifax chief grilled over stock sales | House panel approves B for border wall | Tax plan puts swing-state Republicans in tough spot MORE (Tenn.), Mark KirkMark KirkGiffords, Scalise highlight party differences on guns Stale, misguided, divisive: minimum wage can't win elections Immigration critics find their champion in Trump MORE (Ill.), John McCainJohn Sidney McCainRubio asks Army to kick out West Point grad with pro-communist posts The VA's woes cannot be pinned on any singular administration Overnight Defense: Mattis offers support for Iran deal | McCain blocks nominees over Afghanistan strategy | Trump, Tillerson spilt raises new questions about N. Korea policy MORE (Ariz.) and Lisa MurkowskiLisa Ann MurkowskiRepublicans jockey for position on immigration GOP senator knocks Trump: 'Not a fan of governing by tweet' How the effort to replace ObamaCare failed 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 RubioOvernight Defense: Tillerson, Trump deny report of rift | Tillerson says he never considered resigning | Trump expresses 'total confidence' in secretary | Rubio asks Army to kick out West Point grad Rubio asks Army to kick out West Point grad with pro-communist posts GOP establishment doubts Bannon’s primary powers 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 HarkinThe Hill's 12:30 Report Distance education: Tumultuous today and yesterday Grassley challenger no stranger to defying odds 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 CardinOvernight Cybersecurity: Equifax CEO faces outraged lawmakers | Dem presses voting machine makers on cyber defense | Yahoo says 3 billion accounts affected by 2013 breach Key Dem: Did Kushner use private emails to talk with foreign governments? Dem senator pitches ideas for gun control after shooting 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."