Enbridge (TSX:ENB) had argued to the Federal Energy Regulatory Commission that the petition would give the company the certainty it needed to allow the Sandpiper project to go forward.
But FERC says the filing doesn't meet its regulations for rate changes.
While Enbridge provided 15 letters of support, FERC notes that a number of other companies have protested Enbridge's plan.
The FERC ruling was not unanimous. Two dissenting commissioners said "the order relies on a procedural side-step to avoid making any calls on the merits."
"We are concerned that a significant investment in this nation's infrastructure could be unnecessarily delayed," they wrote.
The Sandpiper project would transport crude from the prolific Bakken oil formation, centred in North Dakota, to Minnesota and Wisconsin.
It is expected to come into service in January 2016.
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