The supertanker was diverted to a UAE port on Wednesday where officials said the damage, which stirred fears of an attack in the strait, was caused by a freak wave.
Forty percent of the world's seaborne oil passes through the narrow Strait of Hormuz, gateway to the oil-producing Gulf, where Al Qaeda has threatened to attack shipping.
Masahiko Hibino, Mitsui O.S.K.'s general manager of tanker safety, told a news conference that reports of earthquake-related waves were difficult to believe.
"There were some media reports saying that strong waves that come with earthquakes may have damaged the vessel...but the doors that were broken were not wet, so that kind of thing is hard to believe."
The company will begin a full-fledged investigation on Thursday.
Hibino also said the company could not definitively say there had been an external attack, nor could it rule out the possibility of an internal explosion on the ship. But he added that there was nothing on the ship to cause such an explosion.
Oman's coastguard cited "a tremor" as the cause of the incident, while an official from the Omani transport ministry said it was "business as usual" in the Strait of Hormuz.
A seismologist in nearby Iran said an earthquake with a magnitude of 3.4 happened in Bandar Abbas.
But Hibino said: "Visibility was not bad, and the wind was calm, according to the crew's report."
"Calm means there were no waves," he added.
He said the crew heard the sound of an explosion, which had then been followed by light.
Japan's Transport Ministry said on Wednesday there was an "explosion" at around 00:30 a.m. local time and cited the possibility of an attack on the ship, but port officials said there was no evidence.
No oil leaked from the very large crude carrier, named M. Star, although Hibino said a member of the 31-strong crew was injured.
The tanker, bound for Chiba, near Tokyo, is carrying around 2.3 million barrels of Qatar Land and Abu Dhabi Lower Zakum crudes, industry sources have said.