"You'll note I've now been president for six and a half years, and we've had some wrangling with Congress in the past. Our service members haven't missed a paycheck," he said.
The comments came after a question on whether the president would follow through on veto threats to the annual defense authorization bill, currently being finalized by House and Senate negotiators.
The White House has threatened to dump the measure over a series of concerns, most notably Republicans' use of temporary war funds to get around mandatory spending caps for all federal agencies.
Obama and Pentagon leaders have argued that even if the move fully funds the military, it hurts national security by short-changing the State Department and other vital agencies.
"What we're not going to do is accept a budget which shortchanges our long-term requirements for new technologies, for readiness," Obama said. "If we shortchange those other priorities, we will be less secure."
Republicans have accused the president of choosing money for bloated government programs over paychecks for service members. Obama's comments cut to that criticism.
The authorization bill, which includes language for a military pay raise of up to 2.3 percent in 2016, is expected to be finalized later this month. That sets up the possibility of a presidential veto in August, just two months before the start of the new fiscal year.
Leo covers Congress, Veterans Affairs and the White House for Military Times. He has covered Washington, D.C. since 2004, focusing on military personnel and veterans policies. His work has earned numerous honors, including a 2009 Polk award, a 2010 National Headliner Award, the IAVA Leadership in Journalism award and the VFW News Media award.