The coal-carrying Shen Neng 1 foundered on the reef on 3 April 2010, leaking tonnes of oil into the protected area.
The accident left a hole in the reef 3km (1.8 mile) long; the ship was stuck for nine days before refloating.
Environmental officials say it could take 20 years for the reef, and its turtle breeding grounds, to recover.
The ship's chief mate had managed just 2.5 hours of sleep in the previous 38.5 hours.
"The chief mate was affected by fatigue and this resulted in a decreased level of performance while he was monitoring Shen Neng 1's position," the bureau's final report on the incident concluded.
"The ship did not have an effective fatigue management system in place to ensure that the bridge watchkeeper was fit to stand a navigational watch," the report said.
The bureau found that the ship lacked proper procedures for planning routes and for handling fatigue.
"Fatigue is one of the key safety risks facing seafarers, and watchkeepers in particular.Safety officials say fatigue caused the ship to run aground on the reef
"Failure to manage fatigue can lead to loss of life, damage to property and damage to the environment," said the bureau's Chief Commissioner Martin Dolan.
"There was a sequence of things going wrong that led to a major failure which is quite often what we find in the course of our investigations," he added.
Last April, the captain, Wang Jichang, 47, was charged with liability for damage to a marine park, while his colleague, Wang Xuegang, 44, was allegedly on watch when the Shen Neng 1 grounded.
The two face large fines and up to three years in prison if found guilty.
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