The charges, laid by Maritime New Zealand, relate to breaches of section 65 of the Maritime Transport Act, which prohibit dangerous activity involving ships or maritime products.
The summary of facts revealed that the charges stemmed from the actions of Hong, the ship's master, and chief engineer Nanayakkara prior to the ship's departure from the port.
Both charges each attract a maximum penalty of 12 months' prison or a $10,000 fine.
According to the summary, the 24,875 gross tonnage ship was due to depart Tauranga shortly after midnight on July 6 bound for China.
As part of the departure processes, the crew undertook testing of the engine, which identified a problem with one of the fuel quantity pistons in the main engine.
The pilot was due to come on board at midnight.
Between 10.14pm and 11.04pm, the crew under the direction of Nanayakkara tested the main engine three times, and each time the number two piston failed.
The failures triggered an automatic slowdown mechanism and sent an alarm to the engine control room and bridge control display.
After the third test, Nanayakkara had the piston cover removed and the piston rod was cleaned, but the same error persisted.
He decided to replace the fuel quality sensor, which triggered an alarm. The work was completed at 23.58pm, and the number two incident control system was reset.
But the engine was not retested.
Nanayakkara told Hong that there had been an issue with the engine and the alarm had been reset and everything appeared to be okay to leave the port.
He then told Hong to override the automatic slowdown mechanism to ensure the engine did not slow down if the alarm was triggered again, which Hong did.
This mechanism is designed to protect the engine in the event of a significant engine fault by sounding an alarm on the bridge and in the engine control room and to reduce or limit the engine speed to 65 revs per minute (rpm).
About midnight, the port pilot came aboard when Hong handed over a pilot card on which he recorded there were no defects affecting the ship's manoeuvrability nor the passage plan and failed to mention the engine issues.
At 12.14am on July 6, the ship started departing the port, and one minute later the same warning alarm was triggered to the engine room and the bridge control unit.
The port tugs let go shortly after the vessel left the dock.
When the pilot requested the ship move to full ahead at 68rpm, Nanayakkara soon realised the same piston had failed again and the engine was not increasing speed.
At the same time, the tidal current had increased to 2.5 knots and soon after to 3.5 to 4 knots and the wind was gusting at 40 to 50 knots and the swell had also increased.
At 12.43am, the pilot called the tug boats to come and assist, and the vessel was pushed to the western side of the shipping channel.
Hong ordered the starboard anchor to be dropped and four minutes later the main engine stopped after the propeller became entangled in a channel marker chain.
The stern of the vessel then slowly swung around in the tide into shallow water where the stern came into contact with the sand.
Tug boats arrived soon after and turned the ship into deeper channel water freeing the stern from the sand and tugged it into deeper water until it could be towed to a safer anchorage about eight hours later.
The vessel remained outside the harbour entrance until July 14, when it was towed into port and it has since departed for Singapore for repairs.
Judge David Cameron remanded both men on bail pending sentencing on September 15.
