Energy:Delegates narrowly voted for a recommendation from the Labour front bench to refer a motion backing the Mayo Shell to Sea campaign to the National Executive Committee (NEC).
The motion, moved by UCD and Dublin South branches, noted that the land of local residents had been handed over to Shell by compulsory purchasing orders to procure the pipeline's construction.
It went on to list negative aspects of the project, and noted that governments led by Fianna Fáil had given corporations involved up to 100 per cent tax write-off.
The motion called on the conference to support the aims of the campaign.
Labour energy spokeswoman Liz McManus agreed that issues of exploration and royalties were important, but she warned delegates that accepting the motion, as it was drafted, would leave the State open to the risk of paying enormous compensation to a private oil company.
"Now I know that is not the intention, but that is the way the motion is framed and I cannot support this," she added.
Ms McManus suggested that a working party be set up to consider all the issues involved, including the impact on local communities. "It is a complex one, and it is important we do not have a knee-jerk reaction," she added.
Graham Ó Maonaigh, Dublin South, a former chairman of Labour Youth, strongly backed the motion.
"Initially, I was sceptical about the campaign, but when I looked into what was involved I became concerned about the safety issues," he added.
"There is no pipeline being built of that magnitude, and scale of pressure, elsewhere." The pipelines in Nigeria were safer than the one proposed for north-west Mayo.
Ms McManus's proposal was carried by 99 votes to 73 on a show of hands.