The head of U.S. Customs and Border Protection (search) announced his resignation Wednesday after overseeing the agency's transition to a front-line component of the War on Terror.

In a statement, Robert Bonner (search) noted he served four years as commissioner — first of U.S. Customs and later U.S. Customs and Border Patrol when his agency became part of the Homeland Security Department (search). Bonner came to Washington the day before 9/11.

"That began my challenge — to secure America's borders from terrorists and other criminals without choking off the flow of legitimate trade and travel, which is so vital to our economy," Bonner said.

His departure has been expected for months. He and Homeland Security Secretary Michael Chertoff have been at odds over issues including whether to transfer control of the civil air patrols over the Washington area from Bonner's agency to the U.S. Coast Guard (search).

In a statement, Chertoff praised Bonner as an "outstanding public servant" who has "greatly enhanced the capabilities of this department."

Bonner's last day in office has yet to be set to allow for a smooth transition, the department said.