Officials said Indian border guards had obstructed "normal activities" on the Chinese side, and called on India to immediately withdraw them.
India also recently accused Chinese troops of incursion on its side.
The area, the Nathu La pass, is used by Indians going for pilgrimages to Hindu and Buddhist sites in Tibet.
The region saw clashes between China and India in 1967, and tensions still flare from time to time.
The BBC's South Asia Editor Ethirajan Anbarasan says the latest development appears to be one of the most serious escalations between the countries in recent years.
Reuters cited Chinese officials as warning the development could "threaten peace".
China has also accused India of obstructing the building of a road in what it says is its side of the boundary.
There has been no official comment from India on the accusations so far.
According to Indian media, there have been tensions between the border guards from both sides in recent weeks, with Chinese troops allegedly crossing into Sikkim and destroying two make-shift Indian army bunkers.
The tensions have already led Beijing to block official pilgrimages across the boundary.
China has accused India of incursion into its territory between Sikkim and Tibet, in a dispute which has raised tensions between the countries.