The Pentagon is "strictly protecting" all budget accounts tied to maintaining the U.S. nuclear arsenal and winding down the over decade-long war in Afghanistan, Carter told reporters at DOD.
That gradual decline will include massive cuts to training for Army units and flight hours for Air Force combat wings that are not preparing to deploy to Afghanistan, Defense Secretary Chuck Hagel said during the same DOD briefing.
Over half of the 66,000 American troops in Afghanistan are scheduled to begin rotating back to the United States this spring, according to the White House.
The remaining 32,000 U.S. forces in country will begin their final draw down after next April's presidential elections.
But on top of those training reductions, the Navy will begin grounding a total of four air combat wings and the department will begin issuing the first tranche of furlough notices to the nearly 800,000 civilian employees at the Pentagon and elsewhere.
However, "we're trying to minimize that in every way we possibly can," Carter added.
The DOD deputy chief made clear the department was not planning on making cuts to programs or people "that are unnecessary, just to do something" about sequestration.
The severe damage those reductions, including that initial tranche of cuts outlined by Hagel poised to begin next week, "is going to be abundantly obvious, starting tomorrow and building through the year," he said.
"Those who do not appreciate how serious this is, as the year goes on, it will be unmistakable. This is not subtle," Carter said. "This is an abrupt, serious curbing of activity in each and every one of our key categories of activity" within the Pentagon.
DOD had spent the better part of a year warning against the significant damage sequestration will have on the military's ability to take on America's adversaries across the globe, in a futile attempt to force lawmakers to find a way to stave off sequestration.
However, some on Capitol Hill have put the blame of sequestration squarely on the Pentagon's shoulders.
DOD's decision to postpone sequestration planning until the last minute, combined with the department's long history of excessive spending and mismanagement on several big-ticket weapons programs, set the stage for sequestration to happen.
"You are part of the problem … you helped cause this," House Armed Services Committee member Rep. Rob Bishop (R-Utah) told DOD officials and top military brass during a panel hearing on sequestration last February.
During the same hearing, Rep. Randy Forbes (R-Va.) asked point-blank whether DOD's decision to not take sequestration into account during its budget planning process was a mistake.
"There's been 560 days since [sequestration] was signed into law as the law of the land ... [and] just within the last couple of weeks, [is] when we've received the memos from you guys about the impacts that this was going to have," Forbes said at the time.
On Thursday, Carter admitted that DOD should bear the same fiscal responsibility as other government institutions and was not exempt from its share of the sequestration load.
"We should only get the money that we deserve and that the nation needs [and] we understand that," Carter said, adding Pentagon strategic planners had built that principle into its new post-Afghanistan national security strategy unveiled in 2011.
To that end, Hagel and Carter said Thursday that strategy, which emphasizes a large-scale shift of U.S. forces from the Mideast to the Asia-Pacific region, will not be sacrificed, as a result of sequestration.
"We're trying to address the national security problems that are going to define this country's future and this world's future. And we're prepared to do that," Carter said.