The finding comes from an Australian Transport Safety Bureau investigation into the grounding at Henry’s Reef in Wreck Bay, off Port Douglas, which occurred just after midnight on September 30, 2017.

The ATSB's interim report, released on Wednesday, raised serious questions about the use of the new electronic chart display and information system (ECDIS).

The crash was severe enough to throw the crew of ABFC Roebuck Bay from their seats and wake the ship's captain.

“The bridge team felt a bump and a shuddering sensation through the cutter’s hull,” the interim report says.

“Almost immediately after, the Roebuck Bay abruptly grounded and came to a complete stop. The officer on watch and lookout were thrown out of their seats onto the display screens in front of them.

“The master, woken by the impact of the grounding, went to the bridge and activated the general emergency alarm. The cutter’s crew mustered, accounted for all personnel and immediately began implementing damage control measures.”

The report also found the ship’s skipper and its navigator had problems saving their amended route through the Great Barrier Reef in the ECDIS in the days before the patrol boat ran aground.

ATSB executive director of Transport Safety Nat Nagy said the reef grounding was being taken very seriously because the new electronic charts were about to become industry standard.

“In July 2018, the installation of an electronic chart display and information system, or ECDIS, became mandatory in almost all large merchant and passenger ships, and they are increasingly being used as the primary means of navigation in the maritime industry," Mr Nagy said.

"Our investigation has been a timely opportunity to explore the operational use of ECDIS with a view to applying any findings and safety analysis to the wider maritime environment."

ATSB investigators have reviewed ECDIS, training and chart compilation as well as running ECDIS simulations and testing ECDIS scenarios during the investigation.

The patrol boat suffered extensive damage to its hull and propellers, needed bilge pumps to pump out water and had to be towed back to Cairns.

The maximum damage occurred to a 990-square-metre section of the shallow reef,  scarred by the Roebuck Bay’s hull as it struck at about 16 knots.

Paint from the Roebuck Bay remains on the reef, but no-one was injured and “there was no reported oil pollution as a result of the incident”.

This new electronic chart system has been compulsory on all large ships navigating the Great Barrier Reef since July 2018.

The review found using the system was complex and has ordered further investigations.

“Furthermore, the effective use of ECDIS for safe navigation relies upon the operator being fully familiar with the capabilities and limitations of ECDIS and electronic navigational charts,” the report says.

The report finds the ship’s captain had 27 years experience as a skipper, the past four years with the Australian Border Force.

He had completed “generic” ECDIS training in July 2014 and further online training in December 2014.

The navigator had 21 years' experience at sea, including five with the ABF. He had “generic” ECDIS training in May 2016 and further online training in December 2016.

The Roebuck Bay was travelling south, negotiating the Great Barrier Reef as it sailed from Saibai Island, near Papua New Guinea, towards Cairns.

It struck Henry’s Reef at 25 minutes after midnight – suffering serious damage - when it was 15 metres to the port of its planned route through the reef.

The amended route had been entered into the new electronic chart display system three days earlier by the ship’s master and its navigator.

The vessel was on auto-pilot as the navigator came on to the watch just before midnight on September 29, however the navigator made some adjustments just before the crash.

The 38-metre vessel ran aground, flooding large storage areas on the patrol boat. As the weather worsened, it was towed off Henry’s Reef to avoid further scraping damage to the reef.

The report shows bilge pumps also failed and spares had to be flown out to the boat as it was being towed back to Cairns.

In September 2016, the Australian government received a $39.3 million settlement from the Chinese owners of the coal carrier Shen Zen 1 which created a three-kilometre scar when it ran aground on the Great Barrier Reef in 2010.

The final report into the incident is due in "first quarter 2019".