President Obama vetoed the annual defense authorization bill Thursday as part of an ongoing fight with congressional Republicans over the federal budget that has left a host of military policy changes caught in the crossfire.

The move puts in doubt whether lawmakers can complete a planned overhaul of the military retirement system and whether a host of military specialty pays and bonuses will be renewed in January. The authorization bill has been signed into law for 53 consecutive years, a rare piece of bipartisan compromise through eras of partisan fighting.

"As president and commander in chief, my first and most important responsibility is keeping the American people safe," Obama told reporters at an unusual veto ceremony at the White House. "And that means that we make sure that our military is properly funded. … Unfortunately, (this bill ) falls woefully short in key areas."

At issue is the $612 billion bill's inclusion of authorizing language for roughly $38 billion in extra overseas contingency funds. Republicans are using the temporary war accounts to get around mandatory defense spending caps for 2016, without lifting caps for non-defense accounts.

Democrats have decried that practice as an unfair and irresponsible budgeting gimmick, and stalled every congressional appropriations measure in the Senate in response.

But a sizable number of House and Senate Democrats broke ranks with that strategy on the authorization bill, which Republicans have said is mostly policy measures and does not directly order the problematic appropriations.

House Armed Services Committee Chairman Mac Thornberry, R-Texas, noted the measure includes authorization flexibility if a broader budget deal is reached, making the president's veto all the more unnecessary.

"It's distasteful," he told reporters earlier this month. "There is nothing more we could have done in this bill to satisfy what the president is worried about."

On Tuesday, after Congress formally sent the bill to the White House, House Majority Leader Kevin McCarthy, R-Calif., called the then-looming veto "not only irresponsible, it just doesn't make sense."

"And the president is even threatening to do this at a time when he has recommitted troops to Afghanistan," McCarthy said in a statement. "Our country and armed forces deserve better."

A congressional override of Obama's veto is unlikely, but House leaders will attempt it Nov. 5.

That chamber easily passed the measure 270-156, but fell well short of the 290 votes needed to override the veto. Senate Minority Leader Harry Reid, D-Nev., said despite enough apparent support from Democrats in his chamber, his caucus would sustain a presidential veto "without any question."

Both Thornberry and Senate Armed Services Committee Chairman Sen. John McCain, R-Ariz., have repeatedly said they don't have a backup plan for the authorization bill. The compromise measure was the result of nine months of debate and negotiations, and any revised or resurrected measure will depend on a larger budget deal between Obama and Republican leadership.

"We have done our job," McCain said. "We won't be in those negotiations. We can't control any of that."

The biggest casualty of a vetoed authorization bill would be the retirement overhaul, under discussion for years among military advocates.

The new plan would replace the 20-year, all-or-nothing current system with a blended retirement deal including a reduced pension and a 401(k)-style investment plan. It wouldn't go into effect until 2018, but it would guarantee most troops leave the service with some retirement benefit.

Hill staffers have warned that negotiations on that issue have been detailed and difficult, and reopening the deal could jeopardize its chances of ever becoming law.

The measure also includes new protections for sexual assault victims in the ranks, a new review of personal firearms for troops on U.S. bases and re-enlistment bonuses that Pentagon officials have said are critical for retention goals.

The veto is just the fifth of Obama's presidency, among the lowest usage rate in U.S. history. Congress has not successfully overridden any of the previous four.