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A new threat for US defense stocks

Patriot missile
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Several American allies that have historically been big customers for U.S. weapons makers are threatening to scale back orders—looking to China and Russia instead.

Turkey recently announced it was ordering a large-scale air and missile defense system from China Precision Machinery Import and Export Corporation instead of picking a system made by an American or European firm. Making things more complicated is the fact that the Chinese company is in violation of U.S. sanctions for doing business in Iran, Syria and North Korea.

Turkey said it will cooperate in building the system with the Chinese firm as a way to help grow its own domestic defense industry.

(Read more: NATO's Turkey looks to China for missile purchase)

Turkey has been very vocal about its displeasure with how the United States has handled the civil war in Syria and wants a more aggressive approach to topple President Bashar al-Assad.

Saudi Arabia this week also voiced its displeasure with Washington over what it calls weak leadership on both Syria and Iran. Saudi Arabia wants the US to be much more hawkish against both countries. Syria's intelligence minister hinted his country would start looking elsewhere for defense and intelligence cooperation.

Ian Bremmer of the Eurasia group believes all of this means trouble for the defense sector.

"U.S. defense companies don't get to focus on the countries that want to buy their technology," he said. "They must focus on allies aligned with the United States."

Bremmer said that Washington's foreign policy has allowed competition from defense makers to come in from other areas. "This could have a very significant impact on American export opportunities," he added.

(Read more: Made-in-USA shipbuilding finds an unlikely ally)

In addition, Egypt is also looking elsewhere for defense contracts. The Egyptians are angry with Washington over its lack of support after the Egyptian military deposed Mohammed Morsi in July.

Yair Reiner covers the defense sector for Oppenheimer. Reiner said it's too early to tell if traditional allies of the US in the Middle East are posturing or if they'll really change their buying habits. But he noted: "[The US has] a real technological edge. Saudi Arabia, Egypt and Turkey won't want to buy suboptimal systems to make a political point over the long term."

(Read more: Iran—the new investment frontier?)

Reiner also noted that possible budget cuts also loom over the U.S. defense sector and pose a short-term risk, especially for contractors.

Despite the threats the sector's biggest stocks have had a great year. Lockheed Martin is up 41 percent, Northrop Grumman is up 55 percent and Boeing 82 percent.

—By CNBC's Jason Gewirtz