Enterprise bargaining talks between the two unions, representing CityCat and ferry crews, and Transdev, the company Brisbane City Council contracts to run CityCats, have stalled.

The strike by some, but not all, CityCat crews will last until 4am Friday.

However it could have a “significant” impact on CityCat and ferry customers, Transdev warned on Wednesday.

Transdev managing director Tilly Loughborough said CityCat services would be running at a “significantly reduced frequency” on Thursday and expected CityCats would be "busier than usual".

“The unions’ decision to take further industrial action and unnecessarily impact our customers is regrettable, particularly because our enterprise agreement negotiations have been moving in the right direction with assistance from the Fair Work Commission,” Ms Loughborough said.

“Transdev remains committed to resolving the outstanding issues, related to a new enterprise agreement with its crew, as quickly as possible.”

The council asked CityCat customers to look at alternative public transport.

“Commuters should consider other transport arrangements including regular bus services which ordinarily service the vicinity of ferry terminals,” a council spokeswoman said.

“Council apologises for any inconvenience and encourages commuters to allow extra travel time.”

For timetable information contact TransLink on 13 12 30 or visit www.translink.com.au

Transdev and the two unions are scheduled next at the Fair Work Commission on Tuesday, February 26.

Negotiation difficulties over wage claims and rostering have already resulted in two CityCat strikes in the past six weeks.

A threatened strike last week was called off at the last minute as a show of good faith by the Maritime Union of Australia and the Australian Maritime Officers Union.

Thursday's strike is a protected industrial action, meaning suitably-timed advice has been given to the Fair Work Commission and CityCat crew employers.