Hundreds of Chinese troops allegedly moved into territory claimed by India ahead of a visit by China's President Xi Jinping last month.
The troops eventually pulled back but tensions persist and last week China expressed concern over plans by India to build a highway along the border.
"We consider China as a very important neighbour," Ajit Doval said at an international security conference in New Delhi.
"But while we would like to take every opportunity to develop the relations to their best extent... we will never be able to make any compromise at the cost of our national security and territorial integrity."
China defeated India in a brief but bloody war in 1962 and their border remains unresolved, with both sides regularly accusing each other of sending soldiers into the other's territory.
Doval, who was appointed by the new government of Prime Minister Narendra Modi, said the two sides should "sit together and resolve our boundary dispute amicably and as early as possible".
"We have to involve and engage them (China) rather than follow the path of exclusive isolation from each other," he said.
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