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 CornynSenate's No. 2 Republican pushing gun bill After meeting with Trump, governors say he's crafting his own ObamaCare plan Cornyn: Border wall 'makes absolutely no sense' in some areas MORE (R-Texas) said ahead of the vote. “I believe Mr. Perez’s record disqualifies him from running this or any other federal agency.”

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Sen. Marco RubioMarco RubioTHE MEMO: Trump takes the fight to Congress Rubio says town halls designed for people to 'heckle and scream' At CPAC, Trump lashes out at media 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 CardinDem super PAC ads pressure GOP senators to back independent Russia probe Dem senator: Don't let leaks distract from real issue of Russian interference Washington-area lawmakers request GAO report on DC Metro 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."