Engineers have discovered a second problem with the MV Isle of Lewis.
Ferry sailings between Stornoway and Ullapool had to be cancelled on Tuesday due to technical difficulties.
Sailings resumed on Wednesday but were heavily delayed.
A spokesman for operator Caledonian MacBrayne said on Wednesday that those travelling on Thursday should also expect delays.
He said as a result of work carried out to repair the first fault on Tuesday night, a further technical issue (a minor cylinder head gas leak) had arisen which, although less serious, could not be left unchecked.
Engineers were to work overnight on Wednesday to investigate the problem.
The spokesman added: "We have been keen to avoid losing any further sailings so it is our intention to carry out the work overnight. Unfortunately she has been unable to make up the time lost this morning as hoped and she is currently scheduled to arrive in Stornoway around 3am on Thursday at which stage work will begin. This means that the first sailing in the morning may be delayed by up to two hours but we feel this is preferable to further cancellations.
"Every effort will be made to minimise the time taken but we want to ensure adequate time is allocated to avoid any further problems. We are continuing to work with the engine manufacturer and other specialists to establish what the cause of these problems is. We apologise for any inconvenience caused."
- Island ferry service running again after engineers repair fault
- Island ferry service cancelled as engineers work to repair fault