The stricter regime comes after a Cameroon-flagged vessel was briefly detained by Taiwan's coast guard earlier this month on suspicion of damaging an international cable northeast of the island.
The vessel was owned by a Hong Kong-registered company with a Chinese address given for its only listed director, the coast guard said previously.
Taiwan fears China could sever its communication links as part of an attempt to seize the island or blockade it.
Flags of convenience allow shipping companies to register their vessels in countries to which they have no link -- for a fee and freedom from oversight.
The coast guard said 52 "suspicious" Chinese-owned ships flying flags of convenience from Mongolia, Cameroon, Tanzania, Togo, and Sierra Leone had been highlighted for close monitoring based on port records and data from Tokyo MOU, a regional multilateral body for port state control.
Of the 52 vessels, 15 were rated a "threat" for various reasons -- including the amount of time they spent loitering or sailing slowly near Taiwan's subsea cables in 2024.
Five, considered to pose the greatest threat, had been active in Taiwan's northern, western and southern waters, and had stayed "within Taiwan's territorial waters for more than 15 days", the coast guard said in a statement.
Taiwanese authorities will monitor for "anomalies" in a ship's AIS (automatic identification system) operation and "fake or misuse of vessel names".
Vessels suspected of "loitering, slow navigation, or anchoring" near subsea cables will be warned by radio to leave the area, the coast guard said.
"If the vessel does not comply, coast guard ships will be dispatched to collect evidence and drive the vessel away," it said.
"Boarding inspections will be conducted when necessary to safeguard Taiwan's maritime and international communications security."
China claims Taiwan as part of its territory and has threatened to use force to bring it under its control.
Taiwan has 14 international underwater cables and 10 domestic ones.
In February 2023, two telecoms lines serving Taiwan's outlying Matsu archipelago were cut, disrupting communications for weeks.
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