Wren Thomas was claiming damages from shipowner Edison Chouest offshore after he was captured off the coast of the African country.
But the case has been kicked out because the Houston court lacked jurisdiction over the company involved, the Daily Comet reported.
The claim could still be fought because US district judge Lee Rosenthal dismissed it without prejudice.
A case against Chevron was dismissed with prejudice, however, meaning an end to that particular lawsuit.
Thomas was seeking unspecified damages under the Jones Act.
He was the master of the 3,286-dwt C-Retriever (built 1999), a supply ship supporting Chevron's platform operations. He was held captive for 18 days in a Nigerian swamp.
The captain said in his lawsuit that he told Chouest and Chevron he was concerned about pirate attacks, which had occurred before.
“Thomas worried that the vessel's age, its lack of speed, and the use of easily-accessed VHF radios to communicate vessel locations rather than more secure satellite phones, made the C-Retriever particularly vulnerable,” the lawsuit said.
According to the lawsuit, Thomas started getting threats over the ship's radio and phone in the spring of 2013, but his Chouest supervisors did not transfer him even after he reported the threats to them and a Chevron area manager.