The MV Loch Seaforth has been taken off the Ullapool-Stornoway route and is likely to be out of service until at least the end of April.
The ferry operator said the vessel will be taken to a repair yard for "major" engine repairs.
The vessel is being taken to the James Watt dock in Greenock and will arrive there on Saturday, April 17.
The MV Isle of Lewis will pick up the day service for passengers and for freight on the Ullapool to Stornoway route from tomorrow.
The overnight freight service has been suspended until further notice.
CalMac said the cause of the engine issue will be "thoroughly investigated, and necessary repairs will be carried out as soon as possible."
A CalMac spokesperson said: “Our immediate priority is getting the night freight service back up and running, which we know is vital for the community and local businesses.”
The operator has apologised to customers for the inconvenience.
However, the Western Isles Council – Comhairle nan Eilean Siar – has said the cancellation of the service is “the latest of a number of issues which have affected the service and prevented island businesses from essential travel.”
Councillor Uisdean Robertson, chair of transportation and infrastructure, named the ferry services as “unacceptable” adding that they put island communities at a “disadvantage.”
He said: “The failure of Calmac to provide an adequate ferry service to our islands is continuing to put our communities at a disadvantage.
"This is unacceptable and not enough has been done to address the problem.”
Mr Roberson also noted that “poor service and inadequate” ferry provision has “seriously affected” the Western Isles over the last few months, particularly in Barra and South Uist where the service has been “unacceptable”, he said.
The council has also asked the ferry operator to compensate island businesses who have been asked to travel to Tarbert.
Alasdair Allan, MSP for nan Eilean Siar said he spoke to CalMac on Wednesday night and Thursday morning about the implications the cancellation had on “several lifeline ferry routes.”
He said he stressed the need to find an “urgent solution.”
Robert Morrison, Operations Director for CalMac said: “Please be assured that we are doing our utmost to find solutions to get the service back to normal.”