The Togolese-registered ship Hongtai was detained by the coast guard on Tuesday after a subsea cable serving Taiwan's Penghu island group in the sensitive Taiwan Strait was cut.
The Hongtai, using a flag of convenience, was crewed by eight Chinese nationals and had Chinese funding, the coast guard said.
The captain, surnamed Wang, was a flight risk and should be detained, the Tainan district court said in a statement.
"Wang destroyed the undersea cable, resulting in the interruption of inter-island communications, which affected government and social functions," the court said in a statement.
"The interruption of communications may cause public danger. The crime is not minor and has caused a certain degree of harm to social security," the court said, ordering Wang's detention.
Wang has denied wrongdoing.
Prosecutors said Wednesday they had prohibited the other crew members from leaving Taiwan during their investigation.
The Hongtai had been spotted "lingering" about six nautical miles (11 kilometres) northwest of Jiangjun Fishing Port and was intercepted by the coast guard after the cable linking Penghu and Taiwan was reported cut.
The digital affairs ministry ordered Chunghwa Telecom to transfer voice communications and internet services for Penghu to other undersea cables to avoid disruptions.
It was the latest in a series of Taiwanese undersea cable breakages, with previous incidents blamed on natural deterioration of the wires or Chinese ships.
Taiwan has 14 international underwater cables and 10 domestic ones.
The coast guard said the Hongtai was among 52 "suspicious" Chinese-owned ships flying flags of convenience from Mongolia, Cameroon, Tanzania, Togo and Sierra Leone highlighted for close monitoring.
Authorities will watch for anomalies in a ship's automatic identification system operation and fake vessel names.
Vessels suspected of loitering or anchoring near subsea cables will be warned by radio to leave the area, and boarding inspections carried out when needed.
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