The captain, surnamed Wang, and his Togolese-registered ship Hongtai have been detained in Taiwan since the incident in the strategically sensitive waterway separating Taiwan and China.
China insists Taiwan is part of its territory and uses a range of tactics, including military and political, to pressure Taipei to accept its claim of sovereignty.
The Hongtai, flying a flag of convenience, was crewed by eight Chinese nationals and had Chinese funding, Taiwan's coast guard said at the time.
Wang was charged with violating Taiwan's Telecommunications Management Act for "destroying submarine cable-related facilities", the Tainan District Prosecutors Office said in a statement.
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 the Penghu archipelago and Taiwan was reported cut.
Prosecutors said Wang knew the ship's electronic charts "marked the location of Taiwan's undersea cables" and that the cable on the seabed off Tainan was a prohibited anchoring zone.
Wang allegedly "instructed the crew to release the anchor claw into the water in the early morning of February 25 with the intention of destroying the undersea cable", prosecutors said.
He also "steered the ship in a zigzag motion above the cable, using the freighter's anchor claw to cut the cable", damaging the undersea cable and affecting communications between Taiwan and Penghu, they alleged.
Prosecutors also said Wang had shown a "bad attitude", denying the allegations against him and refusing to reveal the identity of the shipowner.
If found guilty, Wang could face a maximum seven-year jail term.
Prosecutors said they will not charge the other seven crew members, who will be deported by immigration authorities.
Taiwan has 14 international underwater cables and 10 domestic ones.
There have been a series of undersea cable breakages in recent years, with previous incidents blamed on natural deterioration of the wires or Chinese ships.
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.
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