Members of Congress on Thursday night voted overwhelmingly in favor of a defense bill for 2014 that significantly reforms how allegations of sexual assault within the military are handled.

The National Defense Authorization Act was approved by the Senate with an 84-15 vote and is now headed to the White House for final approval.

The bill adopts a number of adjustments to the ineffective protocol in place for responding to reports of sexual assault. Notably, military commanders will no longer be able to overturn jury convictions, a civilian review will be called if a commander refuses to prosecute a case, and any person actually convicted of sexual assault will now have to face dishonorable discharge or dismissal.

The bill stops short of including a proposal made by Senator Kirsten Gillibrand that would remove authority to investigate and punish from military commanders in sexual assault cases. Gillibrand argues that victims don't trust the current military judicial system and may fear witness retaliation, adding that experienced lawyers ranked as a colonel or higher are better equipped than commanders to decide if a case should go to court. Her opponents say the changes would undermine military's authority and ultimately be worse for victims, some of whom may prefer to avoid a traumatic trial. Her proposal will be voted on as a standalone bill in the coming weeks. 

The defense bill's approval comes just weeks after a Pentagon report found that incidents of sexual assault in the military have been on the rise. According to the Department of Defense, more than 3,500 cases of assault were reported from October to June of 2012 - almost 50 percent more than the amount of cases reported during the same period in 2011. According to the New York Times, sexual assault, which includes rape, sodomy and unwanted sexual contact or the touching of private body parts, is defined as including attacks by civilians on service members and vice versa. Incidents of sexual harassment are handled by a separate department are not included in the estimate. 

The Pentagon says roughly 26,000 people were victims of sexual assault last year. Of those, only about 3,600 victims filed reports and only 1,700 of those cases were resolved. Of 880 suspects facing assault charges, just 238 were convicted. Sexual assault is often underreported and the Pentagon said it believes unreported cases have risen by 35 percent in recent years, so the true figures may be higher. 

The bill also sets aside $552.1 billion for the regular military budget, including a one percent raise for personnel, and $80.7 billion for the U.S. presence in Afghanistan and other international operations. It would also allow more flexibility in terms of transferring prisoners in Guantanamo Bay to other countries, that aren't the United States, but does not mandate a shutdown of the controversial prison. 

The vote on defense bill was delayed by a Senate fight over the President's judicial nominees and other appointment. It took a small compromise to move business forward, but one of the casualties of the deal is Janet Yellen, whose confirmation vote for Federal Reserve Chairwoman will now be delayed until early next year.

Update, 11:00 AM:  President Obama said today that the military will have one year to significantly improve its sexual assault record or face stricter regulation. In a statement provided to the Associated Press, Obama said the military had an "urgent obligation," to protect victims and ensure perpetrators are brought to justice, adding:

If I do not see the kind of progress I expect, then we will consider additional reforms that may be required to eliminate this crime from our military ranks and protect our brave service members who stand guard for us every day at home and around the world.

Obama referred to sexual assault in the military as a "corrosive problem, which is a violation of the values our armed forces stand for, destroys trust among our troops, and undermines our readiness," and continued:

As commander in chief, I've made it clear that these crimes have no place in the greatest military on earth."

Representatives say Obama has not taken a stance on Senator Gillibrand's proposal, but that he supports the change listed in the new defense bill.