The Defence Department said it had advised the government of issues involving possible faults in the exhaust system of Guardian-class patrol boats.
The patrol boats had been sent by Australia to Pacific nations through the Pacific Maritime Security Program.
"It is vital that defects detected during service operation are addressed promptly," a defence spokesman said in a statement.
"Other issues have emerged over the past 16 months and have remediation plans in place. This includes cracking in the coupling between the engine and the gearbox, and ventilation on the sick bays."
Defence officials are set to travel to Pacific nations to assess the patrol boats and to work on rectifying the issue, before coming up with a longer-term solution.
"The Guardian-class patrol boats are the sovereign property of the individual Pacific island nation," the defence spokesman said.
"Each nation will make its own decision on whether they choose to operate the vessels or pause operations."
Mr Marles said it would be critical the boats were fixed as soon as possible.
However, he laid blame for the issue behind the boats at the feet of the former coalition government.
"We're going to work through a program now of making sure we fix them, because they're critical boats for our Pacific partners," he told reporters in Canberra on Friday.
"The fact that the former government was sending broken boats out to the Pacific is a disgrace."
The Pacific Maritime Security Program is a $2.1 billion program supplying 22 Guardian-class boats to Australian Pacific partners.
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