The fees are a counter-measure against upcoming US port fees, it noted.
US ships arriving in China will be charged 400 yuan ($56) per net tonne. That fee will go up to 640 yuan in April and then increase annually.
Each ship will be charged at its first port of call—not at each place it docks—and a vessel will be charged no more than five times a year, the ministry was cited as saying by global newswires.
The charges will be effective on the same day US ports start applying fees for Chinese-built and operated ships arriving there.
The US decision was the result of an investigation by the US Trade Representative into China's shipbuilding sector launched under the previous US administration. There will be separate fees for Chinese-operated ships and Chinese-built ships, and both will gradually rise over subsequent years.
For Chinese-built ships, the US fee starts at $18 per net tonne or $120 per container.
"It is clearly discriminatory and severely damages the legitimate interests of China's shipping industry, seriously disrupts the stability of the global supply chain, and seriously undermines the international economic and trade order," the Chinese ministry said.
ALCHEMPro News Desk (DS)
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