"Secretary Gates is a very deliberate and careful man. He does not make idle threats," Morrell said.
Gates is attempting to cut funding for the C-17 cargo plane and for a new F-35 Joint Strike Fighter engine.
Gates see the programs as unnecessary while lawmakers see them as spending that creates jobs, Morrell said.
The C-17, which Gates tried to kill a year ago, accounts for 30,000 jobs in Missouri, Georgia, Arizona and California, The Washington Post reported Monday.
"That many people employed in an economy that's still suffering ... makes members of Congress reluctant to cut funding for it," said Travis Sharp, a defense industry analyst at the Center for a New American Security.
The House Armed Services Air and Land Forces Subcommittee, led by Rep. Adam Smith, D-Wash., cut funding for the C-17 program last week, but lawmakers are expected to reinstate funding anyway, the Post said.
Gates, however, said he would ask President Obama to veto any defense budget that includes funding for the C-17 or the jet fighter engine.