They want more oversight of the company's onshore gas exploration in the Beetaloo Basin, 500 km southeast of Darwin, and the Barossa offshore gas production project.
Environment Centre NT said the nation's second-largest independent gas producer was attempting to greenwash the Barossa project and is calling on the territory's environment protection authority to fully assess its impact.
"Santos is trying to develop the dirtiest gas field in Australia at Barossa," spokesman Jason Fowler said on Saturday.
"They are literally scraping the bottom of the barrel."
About 40 protesters gathered at Santos's East Arm premises chanting "protect country land and water" while holding placards saying "frack off" and "stop Barossa and Beetaloo gas".
ECNT said documents submitted to the EPA show that two-thirds of the carbon dioxide from the gas field will be vented directly into the atmosphere before the gas is piped to Darwin.
"The gas field has a reservoir CO2 content of 18 per cent, double that of any other Australian gas project," Mr Fowler said.
Tiwi traditional owners are also understood to oppose the Barossa project and the proposed pipeline extension which could cross 100km of open ocean if approved by the environmental protection authority.
"The original environmental approval for Darwin LNG was given by the EPA in 2002 under the now-defunct Environmental Assessment Act," Mr Fowler said.
"The ECNT is calling on the entire Barossa project, not just the pipeline, to be referred for assessment under the Environment Protection Act."
The activists also raised concerns over Santos alleged actions on a cattle station in the Beetaloo Basin.
Landowner Rallen Australia recently accused the Santos of having a "cavalier attitude" to government regulations after it allegedly failed to provide full details about its exploration drilling program on Tanumbirini Station.
The pastoralist claimed Santos withheld information designed to balance the interests of miners and landholders and took the publicly listed energy company to the NT Supreme Court.
The parties ended their battle on January 14 with Santos agreeing to pay Rallen's $400,000 legal bill, reform its stakeholder engagement and stop work at the two controversial exploration wells that caused the legal stoush.
"As the recent high profile court case showed, Santos is an arrogant operator that tries to run roughshod over the rights of locals so it can foist its polluting onshore fracking projects on communities that want nothing to do with the company," Protect Country Alliance spokesman Dan Robins said.
"It isn't only Santos who is guilty of this behaviour – the entire fracking industry has an atrocious record in dealing with others impacted by their polluting and climate destroying activities."
Santos has been contacted for comment.
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