Due to the rampant issues of smuggle and illegal immigration damaged the national and social security and the economic order caused by the unequal governance of coast defense, respectively charged by Ministry of Interior, Ministry of National Defense and Treasury and Farmers' committee, the National Security conference established “Seacoast Defense Patrol Sole Responsibility Organization” on March 18, 1988 to unifies our country coast defense governance, which solved the malpractice and displayed full overall potency.

On January 28, 2000, to effectively manage the waters surrounding the nation, three major departments-the Coast Guard Command of Department of Defense, the National Police Agency Water Police Department and the General Administration of Customs and Anti-Smuggling-were amalgamated to form one body on January 28, 2000. This new Ministerial-level dedicated to law enforcement on the coast and at sea, establishing a unified mechanism for enforcement.

For reengineering government, ongoing consultation and the development of recommendation to reform an innovative, effectives, efficiency, economy, equity and excellent one, Ocean Affairs Council was formally established located in Kaohsiung on April 18, 2018.

Inherited by the 5 Core Missions (Maritime Public Security, Marine Conservation, Search and Rescue, Fishing Rights Protection, Marine Affairs ) of Coast Guard Administration, Eastern Branch has posted successes in coastal waters, smuggling and stowaway crackdowns, maritime rescues, natural resource conservation and public services.