The Scottish Conservatives said it was "another hammer blow" for island communities.
Delivery of two CalMac ferries, Glen Sannox and an unnamed sister vessel, is already running four years late.
Bosses said it was currently "not possible to determine the impact on schedule and cost" of the problem, which affects Glen Sannox, the ferry destined for the Arran route.
Cables installed on the ship in late 2018 or early 2019 are too short to meet the necessary equipment.
This will inevitably have knock-on effects on the schedule for the second vessel, bosses said.
Scottish Conservative transport spokesman Graham Simpson, who raised the issue at First Minister's Questions, said: “This latest fiasco at Ferguson is another hammer blow for island communities, who have had to put up with a sub-standard ferry service under the SNP for far too long.
“Glen Sannox is already years late and this blunder will leave people wondering if it will ever go into service.
“The ship was meant to support one of CalMac’s busiest crossing routes between Ardrossan to Brodick, but this further hold-up means passengers will have to make do even longer with ageing and increasingly-unreliable ferries.
“We need to be told the cost and time implications of the latest blunder at the SNP-owned shipyard, which is in danger of becoming a laughing stock.”
The two ferries are already estimated to be nearly £100 million over budget.
Ferguson Marine was taken into public ownership in 2019.
In a letter to Holyrood's transport committee, Tim Hair, turnaround director of the shipyard, said each ferry relies on a "complex network of cables".
Around 15 per cent of these were installed on Glen Sannox prior to the shipyard falling into administration in August 2019.
Mr Hair said: "It has recently emerged that a large proportion of the legacy cables have not been installed in line with the engineering information held by FMEL [Ferguson Marine Engineering Limited], leaving the free ends too short to connect them to the equipment.
"Initial indications were that this issue was restricted to a small number of cables and a rework and survey process was immediately established to address the problem.
"This revealed the true scale of the problem and the conclusion that 801 [Glen Sannox] will face a delay.
"Investigations are continuing and it now appears that the scale of the problem is such that the best solution is likely to be to cut out most or all the legacy cables and start again with a properly controlled process."
At least 400 cables are affected, although it could be as many as 939.
Details of the revised schedule and project cost are expected at the end of March.
Speaking at FMQs, Nicola Sturgeon said the Scottish Government was "working closely with the yard to ensure that this is rectified as quickly as possible and as cost effectively as possible".