Contractors are back at the Mayfield Road junction - after the new £700,000 signalling system failed on its first day.
The controversial works which have led to town being gridlocked and long tailbacks were finished as planned on Friday but the lights have gone out due to an elecrtical fault.
Temporary lights are now in place again while specialist engineers work on the problem.
A council spokesperson said: “The new junction opened as just before the schools broke up for the summer break, and coped very well with the increased volume of traffic.
“Unfortunately the signals failed on Saturday due to a signalling circuitry fault and temporary lights have been reinstated until the fault is repaired.”
Cllr Don Mackenzie, North Yorkshire’s Executive Member for Highways said: “We are currently addressing the problem and will get the junction up and running as it should as soon as possible.
“We know this must be causing immense frustration for road users and residents in Whitby, but people can be assured we are doing everything possible to resolve the issue swiftly. ”