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The incident, which occurred at a remote, mountainous crossing close to Tibet, is the latest in a long line of border flare-ups between the two neighboring powers.
"Aggressive behavior by the two sides resulted in minor injuries to troops," said the spokesman.
"The two sides disengaged after dialogue and interaction at a local level. Troops resolve such issues mutually as per established protocols," the spokesman added.
Eleven soldiers, four Indian and seven Chinese, were reported to have been injured in the incident, which took place during a patrol in Nuka La, North Sikkim, according to CNN affiliate News18.
The Indian ministry spokesman said "temporary and short" face-offs between troops from both countries are a regular occurrence due to the fact that "boundaries are not resolved."
CNN has requested comment from the Chinese foreign ministry.
India and China share one of the world's longest land borders. In 1962, the two countries engaged in a bloody Himalayan border war and skirmishes have continued to break out sporadically in the decades since.
Though not a part of Indian territory, the area is close to the "chicken's neck," a strategic corridor that serves as a vital artery between Delhi and its far northeastern states.