The 45 kilometre long track is a mecca for runners and has attracted dozens of Bathurst entrants in recent years.

The challenging course winds its way from Katoomba through the Megalong Valley and Coxs River and ends at Jenolan Caves.

Each year around 850 runners enter the gruelling event.

Race director Mohammed Alkhub said damage from the Green Wattle Creek and Gospers Mountain bushfires that raged along marathon route, and subsequent flooding and landslides have left the area damaged.

"The fires were absolutely drastic this year, more than any other year, and it's affected some of the course," Mr Alkhub said.

"The whole back area of Jenolan Caves, including the Two Mile access road to Jenolan Caves, was mostly affected.

"The rains that have come down in the last month or so, they were really heavy and they affected the whole area with land slips and landslides and that meant the closure of the Five Mile access road."

Mr Alkhub said geotechnical assessments were still being conducted on the Five Mile with this road still closed in both directions.

Also, the 54-58 seat coaches that would usually pick up runners after they finish the event are currently not allowed on the Two Mile.

Mr Alkhub said it ultimately came down to runner safety and the race committee had too many concerns about the condition of the track following the fires and floods.

"It was a very difficult decision to make and there was lots of debates between committee members," he said.

Alternatives including ending the event at the 36 kilometre mark were considered.

"We also looked at options like running 20 kilometres in and 20 kilometres back, but in some places it's only a single track so runners would have been obstructed," Mr Alkhub said.

The loss of business and cancellation of accommodation in the area was also a factor in the race committee's decision.

"We encouraged runners to still have a weekend away rather than cancel," Mr Alkhub said.

He said runners were understanding that the event was cancelled and many had posted positive comments on the event's Facebook page.

The Six Foot Track Marathon has been running each year since 1984.

The only other time it was cancelled was in 2012 when the Coxs River was too flooded for runners to pass through.