Washington and Seoul began talks last month on deploying the Terminal High-Altitude Area Defence, or THAAD, system to combat the threat of North Korean missiles, following a recent nuclear test and long-range rocket launch by Pyongyang.
Carter was yesterday speaking on US defence policy toward the Asia-Pacific ahead of a trip to India and the Philippines.
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Both China and Russia oppose the deployment of the THAAD system on South Korean soil. China has expressed concern that it would allow US radar to penetrate in Chinese territory.
Chinese President Xi Jinping reiterated that concern when he met last week with President Barack Obama on the sidelines of a nuclear security summit in Washington.
The US says the system is designed purely to counter the threat of North Korean missiles and would not undermine China's strategic deterrence.
The differences over THAAD are a sore point between Washington and Beijing despite a growing convergence in their approaches toward North Korea, a traditional ally of China.
Beijing in February agreed to the toughest UN sanctions yet to punish the North for its weapons development, and has vowed to implement them fully.
Carter said he hoped China would work more effectively with North Korea to head off the missile threat.
"We need to defend our own people. We need to defend our own allies, and we're going to do that," Carter said in his remarks, which were webcast.
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