Shell declared force majeure on Bonny Light crude, the Nigerian blend, as of May 4.
"The action is due to production deferment caused by incessant crude theft and illegal bunkering on Nembe Creek Trunkline," the company said in a statement.
The shutdown means 60,000 barrels of oil per day is deferred while repairs take place.
Shell Petroleum Development Co. of Nigeria disconnected two sections of the pipeline that is said were the target of oil thieves.
Tony Attah, vice president of health and the environmental for Shell in Africa, said engineers were working on eight other sections considered pilfering points.
"This is a difficult work requiring careful planning and digging up several sections of the line in swamp and land, investigating illegal bunkering points and deciding whether to clamp them or do sectional replacement," he was quoted by Nigerian newspaper This Day as saying.
Shell is accused of causing massive environmental damage in parts of Nigeria. The U.N. Environment Program last year said it would likely take 30 years to clean up oil spilled in the region. Shell is accused of underestimating the volume of oil spilled, though it blames most of the spills on oil bandits.