Capt. Thomas A. Hejl, commanding officer of the Japan-based USS Kitty Hawk, was temporarily transferred to an administrative position in San Diego.
"It is very important that our ships here in the forward deployed naval force are in top condition and that their crews are trained and prepared to carry out their mission," Commander Matthew Brown, a Seventh Fleet spokesman in Japan, told CBS Radio News. "A number of engineering deficiencies resulted in an unsatisfactory material assessment of the ship. Additionally, there were significant equipment casualties and incidents."
A 23-year-old Kitty Hawk crew member was arrested in Yokosuka on August 11 on suspicion of attempted robbery and causing injury, and a 29-year-old crew member was arrested at Narita airport near Tokyo on August 8 on suspicion of smuggling 2.2 pounds of marijuana into Japan.
Four others were arrested in two separate robbery incidents, Japanese police said.
"Over a period of time, there is a body of evidence or information that has come together that showed the ship just was not operating up to the standards expected of it, and they were not improving," said Brown.
The Kitty Hawk collided with a buoy in Singapore earlier this year that damaged one of the ship's propellers and shaft.
The Kitty Hawk normally has 70 to 80 aircraft on board and can carry a maximum crew of 5,500. The Seventh Fleet operates in the western Pacific and the Indian Ocean.
The ship was sent to the Indian Ocean last year to help support the U.S. military response to the September 11 attacks on New York and Washington.
Brown cited the war on terrorism and a possible strike against Iraq as factors in the decision.
Hejl, a native of Boca Raton, Fla., was a Naval aviator and a 1977 graduate of the U.S. Naval Academy.
Brown cautions this is hardly the end of Hejl's career.
"He is a decorated combat pilot and this action should not detract from the fact that he has made such a commitment to his country and to the Navy," he said. " He was relieved of his command but he is still very definitely in the Navy."
Hejl is the second commanding officer on a carrier to be removed in less than a year. Navy officials removed the captain of the USS John F. Kennedy in December when the aircraft carrier failed an inspection.
Hejl will be replaced by Capt. Robert Barbaree Jr., commanding officer of the USS Seattle and a former executive officer of a San Diego-based carrier, the USS Nimitz.
For four decades, the Kitty Hawk was based in San Diego. It relocated to Yokosuka Naval Base in Japan in 1998.