The MV Hebrides returned to service on Monday morning after it required repairs to its carbon dioxide (CO2) firefighting system.
The lack of the vessel meant several key Western Isles routes were cancelled last week, with the MV Isle of Mull being redeployed to cover the shortfall.
Island communities have repeatedly voiced their frustration about disruption to the ferry service in recent months.
Robbie Drummond, managing director at CalMac, said the MV Hebrides’ route was now getting back to normal.
He told the BBC’s Good Morning Scotland programme: “Clearly customers are really upset about the latest disruption of last week and everyone at CalMac is deeply sorry for what they’ve been going through.”
Mr Drummond said CalMac wanted to encourage people to see the “brilliant scenery” of the Western Isles.
He said passenger numbers were down by about 50 per cent compared to 2019 figures.
When it was put to Mr Drummond there was not enough resilience in the ferry network, he said: “There’s no lack of effort or money being invested in short-term resilience.
“Our spend is increased by 70 per cent (over the) last five years, from £21 million to £34m this year.
“But what we really need, and you’re right, is that long-term investment program.
“Because that’s what will give the islands the service they need, and one that we can all be proud of.”
He said he expected the service to remain challenging for the next year, but problems would ease in the coming years when new vessels are introduced.
Two ferries being built at Ferguson Marine in Port Glasgow were expected to have been completed by 2018, but have since been delayed until at least 2023.
Costs for the two CalMac vessels have more than doubled from the £97m price tag.
The apology was issued after it had been reported on the weekend that shops across some Scottish islands were being forced to ration essential items due to the ferry disruption.
South Uist is among locations reliant on a daily lorry crossing to supply shops.
John Daniel Peteranna, from the Lochboisdale Ferry Business Impact Group, had told the Herald on Sunday: "You cannot get more than one carton of milk in each shop.
"It is the milk and the dairy stuff that is the priority. There is no milk produced locally. Maybe that is something we should look at as we seem to be isolated from the rest of Scotland.
"We need to do something different, because the Government isn't interested in helping us. Something needs to change."
Joe Reade, chairman of the Mull & Iona Ferry Committee, last week lodged a complaint to CalMac over the "huge capacity reduction" for both cars and foot passengers that had emerged "in the busiest week of the year" when the MV Hebrides was not running.
He said: "This zero-sum decision demonstrates yet again what an appalling state our ferry service is in.
"For the fleet to be so stretched and fragile, that this is the necessary 'solution' for a breakdown, proves once again that there is a complete failure of strategy and delivery from government and its agencies.”