After an audit led by the bureau’s headquarters in Washington revealed that the agents had not received authorization, the agents asked for permission and got it. The investigation ultimately found no evidence that the protesters were plotting to damage the pipeline, and it was closed.

The Guardian first reported the investigation on Tuesday.

As the F.B.I. changed its focus to national security after the Sept. 11, 2001, attacks, it began building closer relationships with the nation’s largest companies as it worked to protect the country’s critical infrastructure. Many of those companies — like TransCanada, which owns the pipeline — are frequently targets of environmental protests, and issues of free speech and national security can become intertwined.

The F.B.I. said on Tuesday that it had not conducted a full investigation into the protesters — only an assessment, its least invasive inquiry. The bureau said it had looked into the accusations because the threats were against “the oil and gas industry, and the energy sector is considered a part of the critical infrastructure of the United States.”

It characterized the mistake by the agents as an “administrative error” that “was discovered by the F.B.I.’s internal oversight mechanisms.”

“While the F.B.I. approval levels required by internal policy were not initially obtained, once discovered, corrective action was taken, noncompliance was remedied, and the oversight was properly reported through the F.B.I.’s internal oversight mechanism,” the bureau said. “At no time did the review find that the initial justification for the assessment was improper.”