'The commanding officer exercised poor judgement, and the executive officer exercised poor leadership of the ship's training program,' the USS Seventh Fleet said in a statement released in Japan on Wednesday.
A spate of U.S. naval collisions this year has resulted in a major leadership shake up in the U.S. Navy in Asia as it tackles increased tensions with North Korea and engages in operations in the South China Sea that challenge Beijing's growing control of the waterway.
The U.S. Navy in August ordered a fleet wide probe and removed Seventh Fleet chief Vice Admiral Joseph Aucoin, citing a lack of confidence in his ability to command.
Last month Admiral Scott Swift, responsible for U.S. naval forces in the Pacific, said he plans to retire after being passed over for promotion to the chief of all military forces in the region.
The McCain's sister ship, the Fitzgerald, almost sank off the coast of Japan in June after colliding with a Philippine container ship. That incident claimed the lives of seven U.S. sailors.
In May, a South Korean fishing vessel collided with the guided-missile cruiser Lake Champlain, while another guided-missile cruiser, Antietam, damaged its propellers in January while anchoring in Tokyo Bay.
The McCain's captain, Commander A. Sanchez, and his executive officer, Commander J. Sanchez, were reassigned to other duties in Japan, where the Seventh Fleet is headquartered, the Navy said.
The Seventh Fleet operates as many as 70 ships, including the U.S. Navy's only forward-deployed aircraft carrier, and has about 140 aircraft and 20,000 sailors.