Parnell, who is also the assistant to the Secretary of Defense for public affairs, said in a brief post on X that the secretary of the navy is leaving, without providing any explanation for the sudden departure, Xinhua reported.
Under Secretary of the Navy Hung Cao will take over in acting role, the spokesman said.
The announcement came as the US Navy is carrying out a blockade of Iranian ports near the Strait of Hormuz during a ceasefire in the war with Iran.
The Secretary of the Navy is a civilian position that oversees the Department of the Navy and is responsible for policy, administration, budgeting, and overall readiness.
Defense Secretary Pete Hegseth has removed multiple senior military officers across the department since assuming leadership at the Pentagon. In early April, he fired the US Army Chief of Staff Gen. Randy George and two other generals amid the war against Iran.
It's unclear what led to Phelan's departure. Just a day ago, he addressed a major, annual maritime conference -- the Navy League's annual Sea Air Space conference -- just outside of Washington, DC.