The MH-60 Romeo Seahawk from 725 Squadron at HMAS Albatross was damaged onboard HMAS Warramunga while transiting Bass Strait.
It is understood the $57.5 million Seahawk Romeo helicopter had to be replaced before deploying to the Middle East on 9 October after suffering damage. Warramunga's deployment was not affected by the incident.
An initial investigation said one of the lashings securing the helicopter failed.
Defence Connect understands no one was injured in the incident.
The extent of the damage is yet to be confirmed.
A spokesperson for the Department of Defence provided Defence Connect with the following statement: "On 9 October 2017, as HMAS Warramunga was transiting Bass Strait, the embarked MH60R Seahawk helicopter was damaged in a heavy sea state. An initial investigation revealed one of the lashings securing the helicopter failed.
"Investigations into the incident are ongoing."
Australia approved the acquisition of 24 MH-60R Seahawk Romeo naval combat helicopters at a cost of over $3 billion to replace the S-70B-2 Seahawk helicopters. The final delivery of the 24 was completed in July 2016.
The helicopters are largely military off-the-shelf built by Sikorsky and Lockheed Martin and were acquired through the foreign military sales process from the US Navy.
Under the acquisition of these helicopters, Australia's Navy will have the capacity to provide at least eight warships with a combat helicopter at the same time, including Anzac Class frigates and the new Air Warfare Destroyers.
The primary missions of the 'Romeo' helicopter is anti-submarine warfare and anti-surface warfare. Secondary missions include search and rescue, logistics support, personnel transport and medical evacuation.
The Australian government recently applied for a 10-year upgrade program for 24 MH-60R Seahawk ‘Romeo’ helicopters, just one year after receiving the final delivery of the 24 aircraft.