But Extinction Rebellion insists KiwiRail should be held accountable for its part in the coal supply chain.
About 15 protesters walked on to the tracks about 7.30am and headed towards a train that was due to leave the station, meeting it head-on.
It backed away and did not return.
The service was taking coal from Bathurst Resources’ Takitimu mine, in Southland, to Fonterra’s Clandeboye milk factory in South Canterbury.
Several police, including negotiators, were also there.
KiwiRail Dunedin operations manager Jamie McFarland said the protest caused a "massive" disruption to its service, both locally and to the wider South Island network.
"The biggest problem I have is that they have recklessly endangered themselves and also my staff — there are other ways to get your message across."
Extinction Rebellion saw KiwiRail as a "soft target" and he said the protesters should be dealing with the company that dug the coal out of the ground and the company that burnt it.
"We are just the middle guys."
But Extinction Rebellion spokeswoman Jana Al Thea (16) said they were there to hold KiwiRail accountable.
“We’re here to tell KiwiRail to stop hauling coal. KiwiRail is carrying climate-destroying coal to make a profit for the very Government that has declared a climate emergency."
An agreement was eventually reached with the protesters that the coal service would not operate yesterday, but trains carrying other goods, including perishables, continued to pass on a separate track.
A police spokeswoman said the protesters left just after 11am.
None were trespassed and no arrests were made.
"Police’s role is to ensure safety and uphold the law, while recognising the lawful right to protest," she said.
