Both Gates and Admiral Michael Mullen, the chairman of the Joint Chiefs of Staff, acknowledged concern over China's suspension of military contacts with the United States because of the arms sales.
But the secretary said the US arms sales were in keeping with the Taiwan Relations Act, and suggested the improvement in relations between Beijing and Taipei had not diminished the need for them.
"We certainly applaud the growing links between Taiwan and the Peoples Republic," he said.
"Another piece of that is the extraordinary Chinese deployment of all manner of cruise and ballistic missiles opposite Taiwan on the Chinese side of the strait," he added.
"So that's a reality that goes along with the growing other links between the two."
Gates was pressed on the question by Senator Diane Feinstein, a Democrat of California, who was in China last week and said that in meetings with Chinese leaders she was told they had offered to "redeploy" forces threatening toTaiwan.
"Now, I understand the word 'redeploy' isn't 'remove.' And I understand the nature of what's there and the number of troops," she said.
"However, I think that the most important thing we can do right now is establish some military-to-military contact," she said.
Gates said the United States was concerned about China's growing missile, cyber and anti-satellite capabilities, which he said made a strategic dialogue between the two countries all the more important.
Mullen echoed that view, saying China "is increasingly opaque, and these dialogues are absolutely critical to try to understand each other."
"Each time, at least from my perspective, each time it gets turned off, it gets turned off by the Chinese, and then we will go through a period of time where we have no relationship," he said.
The admiral noted that the United States has had no relations with Iran since 1979, "and look where we are."
"And so if I use that as a model, that's certainly not one that we can afford as a country or as a military with China as China continues to grow," he said.