Hovertravel launched two new crafts between Southsea and Ryde during the summer but has had to cancel services over the last few weeks because of the problems.
The company has now set a new compensation policy to offer refunds to customers for technical cancellations.
This could include transferring travel to Wightlink at Hovertravel’s expense or giving two free journeys for each one cancelled.
Yesterday one of the new craft, Island Flyer, suffered a transmission fault at Southsea which will require urgent engineering work.
Until it is bought back into service the Island Express is temporarily being used.
In a letter to customers, managing director Neil Chapman said: ‘We would like to thank you for your continued custom and support and we are sorry for any disruptions you have experienced with us this year as we introduce our new craft.’