The collision occurred in waters off the Diaoyu Islands in September, and Japan has no standing to request compensation, said Xinhua, China's official, state-run news agency.
Ministry spokesman Ma Zhaoxu said the area in which the incident occurred has been part of Chinese territory since ancient times and Japan has "no right" to ask for compensation of about $170,000.
Ma said Japanese officials should "reflect" on their actions during the incident.
After the trawler collided with the coast guard vessels, Japanese officials seized the boat and its crew. They were later released.
A media report said the bill included charges for repairs to "two Coast Guard patrol vessels and for other costs, including official work time spent on repairs."