A company official said on Wednesday that around 8000 barrels per day would be lost due to the latest closure, on top of the 90,000 bpd it is already missing.
Shell has also warned clients that it will be unable to meet its export contracts this month.
The Odeama Creek flowstation in Bayelsa State was shut down on Friday when angry villagers attempted to seize the facility because a power generator provided for them by Shell had broken down.
Shell is the biggest international operator in the Nigerian oil business, exporting more than a million barrels of crude per day at peak capacity.
The latest round of protests in the Niger Delta began on 5 December 2004 when villagers from the ethnic Ijaw fishing community of Kula briefly occupied a series of oil facilities in Rivers State near the Atlantic coast.
Following negotiations with the protesters, Shell has begun to restore production, but two plants - Ekulama I and Ekulama II - are still idle pending the result of safety inspections with 90,000 barrels per day shut in.
Odeama Creek is 30 kilometres to the west of Ekulama. It feeds oil from several wells sunk into the waterways of the Niger Delta into a pipeline serving Shell's massive Bonny export terminal.
The spokesman said that trouble had begun when the Odeama community's power supply cut out.
"The generator was provided by Shell to supply electricity to the community since the area is not on the national grid," he said.
"We have sent engineers to repair the generator but it will take time before it can be put back to use," he said, adding that the firm had begun negotiations with the community to reopen the flowstation.
"The flowstation is in perfect condition. Nothing was damaged. We hope to resume very soon," he added.