The Strangford Lough ferry service was suspended on Friday because of a one-day strike by the 16-strong crew.
Staff have complained about salary levels
Staff complain they are paid thousands less than others doing a similar job.
Spokesman Steve Tweed said negotiations had been going on for the past three years but workers "don't believe their concerns are being taken seriously".
The Roads Service said it was disappointed at the action "three weeks before the outcome of a review into structure and grading is published".
It said in a statement that salaries could be considered after this had been completed.
The Roads Service said the review had been delayed because of a lack of resources which had been beyond its control.
Fast and difficult
The union said the crew have to navigate a fast and difficult stretch of water between the villages of Portaferry and Strangford.
Mr Tweed said the Strangford crew members were on a basic wage of £14,000 plus allowances of about £3,500.
He said that in comparison, the crew of the Rathlin Island Ferry, operated by Scottish company Caledonian MacBrayne, were paid a basic wage of £29,000.
The Strangford-Portaferry crossing only takes eight minutes by ferry, cutting out the need for a 75km journey between the villages by car.
The ferry leaves every 30 minutes, and can carry 28 cars.
The service will resume on Saturday.