By Emelie Rutherford

The Senate in a 93-4 vote approved yesterday the confirmation of Raytheon [RTN] executive William Lynn to be deputy defense secretary.

Sens. Claire McCaskill (D-Mo.), Tom Coburn (R-Okla.), Charles Grassley (R-Iowa), and John Cornyn (R-Tex.) voted against confirming Lynn, who has come under scrutiny because he lobbied Congress for Raytheon until last year and because of his work in the Clinton Pentagon.

The early-evening vote followed nearly three hours of on-and-off debate that was dominated by a denunciation of Lynn’s past performance as Pentagon chief financial officer by Grassley, who is the Senate Finance Committee ranking member. Coburn also spoke on the Senate floor yesterday against confirming Lynn.

Senate Armed Services Committee (SASC) Chairman Carl Levin (D-Mich.) and committee members Sen. Jack Reed (D-R.I.) and Jeff Sessions (R-Ala.) spoke favorably about Lynn. McCaskill serves on the SASC.

The White House has issued a waiver allowing Lynn to bypass President Obama’s new ethics rules banning government appointees for two years from working for agencies and on issue areas they lobbied, and from participating in matters related to their former employers.

Lynn has pledged to recuse himself for a year from six Raytheon programs for which he lobbied Congress in 2007 and 2008: the DDG-1000 surface combatant, the Advanced Medium- Range Air-to-Air Missile (AMRAAM), the F-15 airborne laser, the Patriot “Pure Fleet” Program, the Future Imagery Architecture system (which has been terminated), and the Multiple Kill Vehicle.

The Senate confirmed on Monday three of Obama’s other Pentagon nominations: Robert Hale, the new Pentagon comptroller and chief financial officer; Michele Flourney, the new under secretary of defense for policy; and Jeh Charles Johnson, the new Pentagon general counsel.

Lynn also faced resistance following his confirmation hearing from SASC Ranking Member John McCain (R-Ariz.), who quizzed the nominee on Raytheon matters he will have to recuse himself from because of his past lobbying.