The 10 smaller River Class ferries have been in testing for nearly a year, with the first boat brought into customer service in October.
Some 43 defects were found across the vessels when they arrived, the NSW government said in response to a question on notice from budget estimates.
Most of the defects have now been rectified, the government said.
However, that does not include wheelhouse modifications necessary to be able to use the vessels at night.
Opposition Leader Chris Minns on Monday said the defects were the "latest result of (the government's) offshoring policy".
Labor has been critical of the government's decision to build the ferries in Indonesia, though the government points out they were designed by a Sydney-based company.
Systems design and engineering was also completed by an Australian company.
"The failures on the NSW government's overseas-built Transport projects just keep coming," Mr Minns said in a statement.
"These ferries will end up being two years too late and are riddled with defects.
"Building these ferries in NSW would have created hundreds of jobs and supported our local manufacturing industry. Instead the government decided it would be better to send those jobs overseas."
The Australian Maritime Workers' Union says the latest development is evidence the government's transport procurement policies have failed.
"AMWU members can build our public transport infrastructure," Acting State Secretary Robyn Fortescue said.
"But their skills have been written off by Liberal premiers and transport ministers who continue to go with the option they say is better value for our state."
Transdev, the company which funs the ferries, says 39 of the 43 defects identified were fixed by the supplier under warranty.
The other four are minor improvements which will be considered when the vessels are due for a service.
"Improvements like these are a normal part of any commissioning process," a Transdev representative said.
"Transdev is responsible for the cost of maintaining and operating the new River Class fleet. There are no additional costs for taxpayers."
The River Class ferries have been plagued by problems.
They are too high to have passengers seated on the top deck as they pass under two bridges on the Parramatta River, and are not currently safe for night-time travel.
Issues with transport infrastructure in NSW are not limited to ferries: in recent months, cracks have been discovered in a new Manly ferry and on Sydney's inner west light rail line.
AAP has contacted Transport for NSW for comment.
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