Friday's race was due to start in Doncaster at 2.10pm with a predicted finish time at Harrogate as late as 7.21pm.
The riders were facing an 186.9 kilometre route including three laps of the Harrogate circuit used for all this week's races.
But the start time has now been revised to 2pm and one lap of the circuit has been removed, reducing the overall distance to 173km.
The changes reduce the risk of the race finishing in near darkness.
A statement from world cycling's governing body, the UCI, said: "This action has been guided by the concern to ensure the security of the riders while preserving the sporting interest ofthe event and the high quality of the broadcast production."
"The expected finishing time of the first rider, based on a 40kmh speed, is now 6.35pm.
The decision comes after a dramatic third day of the championships was disrupted by heavy rain.
The start of Tuesday's women's elite time trial was delayed to allow standing water to be cleared from the course following a series of crashes in the earlier men's under-23 event.