The vessel and the Glen Rosa were first ordered in 2015 and were due to have been ready in 2018.
Both were expected to cost £97 million, however the final bill is likely to be closet to £400m.
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In an interview with the BBC’s Good Morning Scotland, the First Minister was asked if he thought the Scottish Government had served the country’s island communities well with the handling of the fiasco.
He replied: “Obviously, I regret very much the cost that’s been involved and the delays that have been involved in the Glen Sannox and the Glen Rosa.
“These ferries should have been built a great deal faster than they were built, and I apologise unreservedly to island communities for the delays in those two ferries.”
Asked if Transport Scotland and the publicly owned ferry operator were fit for purpose, Mr Swinney said: “We undertook some work on this, and the government is looking at the best deployment of resources in this area.
“But what we’ve got to focus on, what I’m entirely focused on, is making sure that islanders have the ferry services that they require.
“I use the CalMac ferry network on a regular basis. It’s a network with which I’ve got a very close association, and I have a huge amount of admiration for the work that goes on in that network to support our island communities, and our communities must be well supported.
“So we have the two ferries coming from Fergusons.
“We’ve also got four ferries that are under construction in the Cemre yard in Turkey.
“Unfortunately, because of the global supply chain issues, the first of those ferries is taking a bit longer than we would have ideally liked, but we are investing in the ferry fleet to make sure that island communities are well supported and they can be assured of the commitment of the Scottish Government to make sure that that is the case.”
When it enters service next month, Glen Sannox will be able to carry 127 cars compared to about 90 for Caledonian Isles, which currently serves the route.
However, the size of the ship also means it cannot berth at the usual mainland harbour at Ardrossan until a major redevelopment takes place.
The ship was handed over to CalMac by Ferguson Marine in November, seven years after the hull was launched from the Port Glasgow yard.
Planned passenger trial runs of the Glen Sannox were delayed because the sewage system on board needed “minor remedial work.”
A number of other “technical issues” were also identified, including those related to the electronics installed in the vessel’s bridge.