The CGA is considered a civilian law enforcement agency under the administration of the Ocean Affairs Council of the Executive Yuan, though during emergencies it may be incorporated as part of the Republic of China Armed Forces.

All mobile investigative groups of the Coast Guard Administration are tasked to perform intelligence-gathering mission of State Security.

While executing such intelligence-gathering function, The Coast Guard Administration is subjected to the supervisory and coordination from the National Security Bureau.

[7] During the 36th annual Han Kuang exercises they participated alongside special operations units from other branches in anti-decapitation drills.

[12] It has seen a great deal of action for a young agency, participating in numerous search and rescue and anti-smuggling operations.

The Coast Guard Administration was also recently involved in escorting Taiwanese fishing boats into waters disputed with Japan claimed by both sides as part of their exclusive economic zones.

[5] In the late 2010s, China escalated to grey-zone actions against Taiwan in an attempt to achieve unification with the self-governing island.

[14] China's grey-zone operations against Taiwan in the maritime domain are meant to establish presence while maintaining plausible deniability.

[20] On March 16, 2020, the patrol boats CP-1022 and CP-2006 of the 9th Offshore Flotilla based on Kinmen were attacked by ten Chinese speedboats.

They had been assisting a Kinmen County Government Fisheries Research Institute patrol boat in clearing fishing nets illegally left in Taiwanese waters by Chinese fishermen when they came under attack from the men in speedboats throwing rocks and bottles.

[26] In May 2022 an Anping-class patrol ship launched a Hsiung Feng II anti-ship missile for the first time in a joint exercise with the Navy.

[28] The CGA cooperates with Japan, the Philippines, Malaysia, Thailand, Indonesia, and Vietnam in operations to counter human trafficking and drug smuggling.

The CGA and the US Coast Guard cooperate on monitoring longline fishing, maritime law enforcement, human trafficking, and drug smuggling.

[31] In May 2021 US President Joe Biden praised the cooperation agreement while speaking at the commencement of the United States Coast Guard Academy.