The company said on Facebook the previous timetable between Seatoun and Days Bay in Eastbourne would not be resuming.
“This was a difficult decision to make as we understand the inconvenience caused for those who were previously using the service, especially those travelling to Scots College.”
“We apologise to those who will be affected by this decision.”
Scots College is a private school in Strathmore Park, which is within walking distance of Seatoun.
The ferry service was a popular choice for students living in Eastbourne to get to school, especially because the two locations are on opposite sides of the harbour.
One Eastbourne resident, who had a child at Scots College last year, said she was disappointed.
“Parents weren’t consulted and provided any options as to whether they were prepared to pay more to maintain the service.
“Scots College is now co-ed and is growing its roll. Was that even considered in the feasibility analysis?”
East by West Ferries said the decision was made due to several factors including the price of diesel, a likely change to passenger volumes, and because only one of their boats will work with the refurbished Seatoun wharf across all tides.
“All of which mean that providing the previous service is no longer practical within what we can reasonably charge to recover costs.”
The decision had not been announced earlier because the company was also considering other related timetable options, East by West Ferries said.
The company was looking at an opportunity to drop in at Shelly Bay, where a development including 350 new homes is taking shape.
“This stop will only add five minutes to our current service, and is relatively easy to add into sailings in both directions across the harbour – giving an alternate to the previous Days Bay - Seatoun service.”
East by West Ferries has also investigated a commuter service between Seatoun and Queens Wharf in the central city.
The company believed a dedicated ferry, with five return services per weekday, had strong potential.
It was hoped this service could have started in February, but more work needed to be done with Metlink.
The company said Seatoun could be included in weekend sailings, which it would review in the coming months.