Adm Scott Swift, the commander of the US Pacific Fleet, relieved Aucoin from duty at the US Navy's Yokosuka naval base in Japan, a US Navy spokesman said.
The warship's collision was the second in about two months, after the USS Fitzgerald struck a Philippine-flagged container ship on June 17.
"While each of these four incidents is unique, they can not be viewed in isolation", Swift said earlier.
Daniel Paul Goetz, from US-headquartered cybersecurity firm Lantium, added that causing a collision would be complicated, as it would involve knowing the exact location, speed and bearing of both ships involved.More news: Real Madrid star Ronaldo invites Ramos anger over Florentino recommendation
Swift said the search at sea would continue despite the discovery of remains in the ship. The Navy did not say how many bodies were found.
An official Chinese newspaper said yesterday the US Navy's latest collision shows it is becoming an increasing risk to shipping in Asia despite its claims of helping to protect freedom of navigation.
The John S McCain's sister ship, the USS Fitzgerald, nearly sank off the coast of Japan after colliding with a Philippine container ship on 17 June. "As such, I've directed an operational pause be taken in all of our fleets around the world", said Adm. Richardson.
In February, the USS Antietam, a guided-missile cruiser, ran aground near the USA base in Yokosuka, Japan, and in May the USS Lake Champlain, another Ticonderoga-class guided-missile cruiser, crashed into a South Korean fishing boat. The subsequent investigation led the Navy to relieve the Fitzgerald's commanding officer and several others of duty over the crew's actions.More news: Two die in quake on Italian island
Jacob Drake, 21, of North Lewisburg, Ohio, was among the missing, according to a cousin, Brandie Roberts. But his relief from command shows the Navy's focus on accountability in the wake of the incidents this year involving the USS John S. McCain, USS Fitzgerald, USS Lake Champlain and the USS Antietam.
U.S. Rep. Rodney Davis, R-Ill., said he had spoken with the Palmer family and would monitor the Navy's investigation into the crash.
While diving proceeds, vessels and aircraft from the Royal Malaysian Navy and Republic of Singapore Navy are engaged in search and rescue activities at sea along with U.S. Navy MH-60 Seahawk helicopters from amphibious assault ship USS America.
The McCain and the tanker ship collided Monday east of the Malacca Strait, the fourth time a USA warship has been involved in an accident in Asian waters this year.More news: Meet Bill Cosby's new legal team for his second trial