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 CornynTrump gets chance to remake the courts Lawmakers eye early exit from Washington Victims of Nazi Art theft need Congress to HEAR 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 AlexanderLamar AlexanderThis week: Government funding deadline looms Key Republicans ask Trump to keep on NIH director McConnell tees up medical cures bill MORE (Tenn.), Susan CollinsSusan CollinsSenators crafting bill to limit deportations under Trump Cornyn: ‘Virtual certainty’ Sessions and Price will be confirmed Trump's wrong to pick Bannon or Sessions for anything MORE (Maine), Bob CorkerBob CorkerExxonMobil CEO, retired admiral will meet with Trump about State: report Conway: Trump expanding secretary of State field 'Apolitical' Petraeus says he did not vote in election MORE (Tenn.), Mark KirkMark KirkJuan Williams: McConnell won big by blocking Obama Battle for the Senate: Top of ticket dominates The untold stories of the 2016 battle for the Senate MORE (Ill.), John McCainJohn McCainA Cabinet position for Petraeus; disciplinary actions for Broadwell after affair Meet Trump’s ‘mad dog’ for the Pentagon Wrestling mogul McMahon could slam her way into Trump administration MORE (Ariz.) and Lisa MurkowskiLisa MurkowskiPassing US-Canada preclearance would improve security and economy Overnight Energy: Dakota pipeline standoff heats up Trump's wrong to pick Bannon or Sessions for anything 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 RubioJuan Williams: McConnell won big by blocking Obama The ignored question: What does the future Republican Party look like? Graham to roll out extension of Obama immigration program 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 HarkinGrassley challenger no stranger to defying odds Clinton ally stands between Sanders and chairmanship dream Do candidates care about our health or just how much it costs? 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 CardinBen CardinAide: Trump invited Philippine leader to WH Dem senator: Hold hearing on Russian interference in election Overnight Finance: Questions swirl around Trump's plan for his business | Treasury pick promises major tax cut | White House downplays Carrier deal 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."