For months, the U.S. has been helping Arab allies coordinate arms shipments to rebel fighters in Syria. Unfortunately, most of those weapons are going to radical Islamists instead of secular opposition groups. According to a classified government report uncovered by The New York Times' David Sanger, the flood of Saudi and Qatari weapons into Syria is strengthening the hand of extremist groups in the country, including those with ties to Al Qaeda. “The opposition groups that are receiving the most of the lethal aid are exactly the ones we don’t want to have it,” a U.S. official says. Not only is there the fear that the weapons could bolster anti-American insurgent groups, but these extremist groups could hold sway in a future Syrian government should President Bashar al-Assad be removed. “The longer this goes on, the more likely those groups will gain strength,” a Middle East diplomat tells the Times.

RELATED: Will the U.S. Take On Syria Next?

It's the sort of dark irony reminiscent of the Soviet war in Afghanistan, in which an influx of foreign militants and weaponry to the mujahideen gave rise to blowback, and even provided a springboard for more ambitious extremists like Osama bin Laden. As it stands, the U.S. is not sending arms directly to Syrian opposition groups, it's reportedly just helping Saudi Arabia and Qatar do it with lighter weapons like rifles and grenades. But this latest assessment, which Sanger says has been delivered to President Obama, calls into question the White House strategy of indirect intervention.

RELATED: Seattle Cops on Twitter, Skulls, and Hunting

That's not to say that the alternatives are great. So far, 25,000 Syrians have been killed in the conflict, the borders of NATO ally Turkey have been threatened and the opposition has been badly outgunned. But no one can say with any certainty whether giving more sophisticated weaponry to the opposition would allow rebels to overthrow the regime or simply increase the bloodshed.

Story continues

RELATED: Would It Be Cheaper to Bribe the Taliban?

While the Obama administration's handling of the Syrian civil war has become an issue in the presidential campaign, it's not clear what Mitt Romney would do differently if elected. Last Monday, he told an audience at the Virginia Military Institute that he would give the rebels who "share our values" the weapons they need to "defeat Assad’s tanks, helicopters and fighter jets,” which suggests he may approve the transfer of antiaircraft and antitank systems.

RELATED: Karzai Picks Fight with Petraeus Over War Strategy

Obviously, no one thinks these Islamist groups "share our values," but it's proven extremely difficult to ensure that fundamentalists don't get their hands on these weapons. It's not clear exactly how many foreign jihadists have entered the fray, but last month, the United Nations' International Commission of Inquiry said it believed there was "an increasing presence of foreign elements, including Jihadist militants, in Syria" who have been radicalizing the rebels. Others say the influx of foreign militants has been marginal. Emile Hokayem, a senior fellow at the International Institute for Strategic Studies, told CNN "They are realistically about 2,000-3,000 in number. Foreign fighter does not equate with jihadi. Not everyone is driven by jihadi ideology."