The commanding officer of the Pearl Harbor-based Virginia-class fast-attack submarine USS Mississippi was relieved of his duties Friday due to a loss of confidence in his ability to command, the Navy said.

Cmdr. Tory Swanson was removed from his position by Capt. Harry Ganteaume, commander of Submarine Squadron 1. A command investigation into the circumstances leading to Swanson’s relief is ongoing, the Navy said.

Cmdr. Brook DeWalt, a spokesman for the Pacific Fleet Submarine Force, said he was limited in what he could say, but that the removal "was a matter of professional nature — not a personal transgression or anything like that. It’s issues revolving around operational decision-making."

Swanson, who had served aboard Mississippi since April 2013, has been administratively reassigned to the staff of the sub force, the Navy said.

The Mississippi arrived at Pearl Harbor on Nov. 25, the fourth new Virginia-class submarine to be home-ported in Hawaii. The Navy said it was "a tangible manifestation of the Pacific Rebalance, and further exemplifies the importance we place on the Asia-Pacific region."

Pearl Harbor is the sole Pacific home for Virginia-class subs, which cost an average of $2.7 billion, according to the Congressional Research Service.

The 377-foot Virginia-class submarines are capable of very precise slow-speed control.

With the Virginia-class vessels, the submarine force gains greater undersea capability in the littorals, or offshore seas, where a lot of quiet foreign diesel electric subs operate.

A native of Arvada, Colo., Swanson enlisted in the Navy in 1989. He earned a Navy ROTC scholarship to Purdue University and graduated in 1996 with a major in pre-law/interdisciplinary engineering.

Swanson served as engineering officer onboard the submarine USS Greeneville out of Pearl Harbor from August 2003 to January 2006. During that time he completed Western and Eastern Pacific deployments, including the first forward deployment of the advanced SEAL delivery vehicle, a one-of-a-kind SEAL commando mini-sub that rode attached to its larger Los Angeles-class submarine host.