The fire brigade is understood to have been called to monitor the situation, as smoke was seen to have come from the vessel.
The service between Sconser and Raasay has been suspended since around noon on Thursday while a charter vessel was supporting passengers and a relief ferry is being deployed.
CalMac has confirmed that the smaller MV Loch Tarbert, which can take on 142 passengers and 17 cars was drafted in the following day to take up some of the slack. MV Hallaig can take 150 passengers and 23 cars.
Because MV Loch Tarbert has been redeployed from the service from Kilchoan to Tobermory on Mull – CalMac have had to charter another vessel from Staffa Tours.
And CalMac has warned users that no vehicles can or will be carried on this route.
The Scottish Government-owned ferry operator said that while it was covering, period advance ticket sales online are not available and that tickets must be purchased at the time of travel.
CalMac are still waiting for confirmation of when MV Hallaig will return to service and said that MV Loch Tarbert will remain in place for the time being.
Highland councillor Angus MacDonald said in response to the move: “Once again enormous disruption to communities caused by the very old ferry fleet.”
The Liberal Democrat added: “Come on Transport Scotland, fund the Calmac replacement needs!”
It was understood that boats were picking up customers on either side of the crossing Sconser to Raasay crossing while the service was suspended on Thursday.
A rigid inflatable boat (rib) was arranged by CalMac to use as passenger charter to transport passengers on the route.
Dan Corigall, who runs Stardust Boat Trips, said he helped get one group of 12 off Raasay on Thursday night and criticised CalMac’s response.
He believed the breakdown left about 40 visitors waiting for help on Raasay. The breakdown also hit locals who had travelled to Skye on shopping trips. CalMac refuted claims people had been stranded.
The MV Hallaig was hailed as the first of two roll-on, roll-off ferries that will run on diesel and electric power, leading to 20% lower emissions.
It was launched from the Ferguson shipyard in Port Glasgow after a £20 million investment in the green technology.
Deputy First Minister Nicola Sturgeon said when it was launched that it was a “great day for Clyde shipbuilding”.
A Transport Scotland spokesman said: “We recognise the impact that delays and disruption has on our island communities and we are fully committed to investing in our ferry services.
“We appreciate that every cancelled sailing can have a significant impact and continue to work with operators and CMAL to improve reliability and resilience across our networks.
“Delivering six new major vessels to serve Scotland’s ferry network by 2026 is a priority for this government. Should there be cancellations to CalMac services due to weather or technical issues then a full refund will be provided to the customer.”