Construction of the Dakota Access Pipe Line (DAPL) was stopped on December 4, 2016 because the Secretary of the Army Corp of Engineers denied a required permit stating that alternate routes need to be studied. I am not clear on exactly what the basis for that decision is but my question is more basic, can the President in his capacity as Commander in Chief simply order the Army CoE to approve the permit?
A civilian leader in the Army made the decision to deny an easement to the controversial Dakota Access oil pipeline despite Army Corps of Engineers recommendations that it be granted, according to officials and a document.
But because of the pipeline's size — 30 inches in diameter — its approval went to Assistant Secretary of the Army for Civil Works Jo-Ellen Darcy, an official said.
When asked why Assistant Secretary Darcy decided to go against the Corps of Engineers recommendation, Kelley her spokesperson said, "the Army decided that the totality of circumstances call for additional analysis, a more robust consideration of alternatives, and additional public information."
Army Secretary Eric Fanning was "supportive" of Darcy's decision but ultimately the decision was hers, the spokesperson said.
President Barack Obama appointed Darcy to be Assistant Secretary of the Army (Civil Works) in August of 2009.
Darcy is therefore a political appointee of Barack Obama, and the Department of the Army most certainly is not considered an independent agency Link (Wiki), but rather part of the federal executive departments, and therefore falls under the President's direct chain of command as both Commander in Chief of the Armed Forces and titular head of the Executive Branch according to Article 2, section 2 and 1 of the Constitution, respectively. While she has enough authority to make the decision, it easily could have come from anyone in her chain of command up to including the President.