The train was stopped a few kilometres from the port when passing Sandgate, near the Pacific Highway, about 10am on Sunday.
About 20 people linked to so-called climate defence group Rising Tide scaled the train and used shovels to unload coal from the laden wagons, while another 30-odd provided support inside the rail corridor.
About 50 people were arrested and moved out of the rail corridor, a spokeswoman for the group told AAP.
Most were given future court attendance notices and released, but four were taken away by police.
The train was stopped for at least four hours.Â
Local police are expected to address media on Sunday afternoon.
Those involved in Sunday's protest said civil disobedience was the only option when NSW was significantly expanding its coal production.
Eight NSW coal projects awaiting approval this year would produce carbon emissions equivalent to 10 times the state's annual CO2 budget, advocacy group Lock The Gate said in February.
"Rallies and campaigning within the system are clearly not working, so people like me who are terrified for our future are left with no option but civil disobedience," renewable energy engineering student Jasmine Stuart said on Sunday.
"As the head of the UN said, the truly dangerous radicals are the countries that are increasing the production of fossil fuels."
Newcastle is the world's largest coal export port, with thermal and metallurgical coal making up most of the $71 billion of goods passing through each year.
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