The area around 100 miles (160 kilometers) from Taipei will be closed from 9 a.m. (0100 GMT) to 3 p.m. (0700 GMT) on Sunday, the Fujian province maritime safety administration said, adding that ships will be "forbidden to enter."
The restrictions to maritime activity in the area come amid a period of escalated tensions between China and Taiwan.
Last weekend, Beijing held three days of large-scale military exercises involving simulated multiple targeted strikes and a blockade of the island which it claims as its own. China has vowed to bring Taiwan under its control, by force if necessary.
Japan's government sought an explanation from China on Wednesday.
"The government is continuing to collect and analyze detailed information, including the communication with the Chinese side, and will take appropriate measures based on the results," Chief Cabinet Secretary Hirokazu Matsuno said.