The Senate confirmed two of President Obama's executive nominees Thursday, the latest development after senators reached an agreement to avert the use of the "nuclear option" earlier this week.

The Senate voted 59 to 40 to confirm Gina McCarthy as administrator of the Environmental Protection Agency and 54-56 to confirm Tom Perez as the next secretary of labor.

McCarthy, who is currently head of the clean air division at the EPA, and Perez, who was assistant U.S. attorney general for the Civil Rights Division, were both nominated by President Obama in March, but their nominations were held up by Republican objections until a deal was struck earlier this week.

Under the compromise, Republicans agreed not to filibuster a group of Obama's nominees in return for Democrats submitting new nominees for the National Labor Relations Board.

Sen. Joe Manchin, D-W.V., was the lone Democratic senator to vote against McCarthy's confirmation, arguing that he would cast a no vote based on the agency itself and its handling of the coal industry.

"My fight is not with her. My fight is truly with the agency itself, the EPA," Manchin said on the Senate floor Thursday. "It doesn't matter that much really who's sitting as the administrator of the EPA. In fact, if the president plans to use the EPA to regulate the coal industry out of existence it really doesn't matter. It could be Ms. McCarthy or someone else because it is the president who will be calling all the shots, and the administration. that's my fight."

Earlier in the day, ahead of the Tom Perez vote, several Republican lawmakers took to the Senate floor to argue why Perez should not be confirmed as labor secretary.

"Americans of all political persuasions have a right to expect that the head of such an important federal department, whether appointed by a Republican or a Democrat, would implement and follow the law in a fair and reasonable way. I do not believe they could expect as much from Mr. Perez, and that's why I'll be voting against him today," Senate Minority Leader Mitch McConnell said.

"He has demonstrated throughout his career that he's willing to, in his words, to push the envelope to advance his ideology," Sen. Lamar Alexander, R-Tenn., said.

On Wednesday, the Senate voted to move ahead on Perez's nomination with a vote of 60-40, just one day after Senators reached a deal to avert the use of the "nuclear option."

Perez is the son of immigrants from the Dominican Republic. He has been assistant U.S. attorney general for the Civil Rights Division since 2009 and previously served as secretary of Maryland's Department of Labor. Former Labor Secretary Hilda Solis resigned from the post in January. Perez's confirmation makes him the only Latino in President Obama's second term cabinet.

Earlier this week, the Senate confirmed Fred Hochberg as president of the Export-Import Bank and Richard Cordray as the head of the Consumer Financial Protection Bureau.