Executive Order (EO) 13337 delegates to the Department of State (the Department) the authority to receive applications for Presidential permits for cross-border facilities and outlines a process for the Department to determine whether granting such permits would be in the national interest. On November 10, 2011, the Department concluded that it required more information before a determination could be made regarding the Keystone XL pipeline application for a Presidential permit. The time period provided in the Temporary Payroll Tax Cut Continuation Act of 2011 is not adequate for the Department to conduct the necessary analysis to gain the additional information.
The Department therefore recommended that the President determine that the permit application for the Keystone XL pipeline filed on September 19, 2008 (including amendments) be denied and that he determine the Keystone XL pipeline, as presented and analyzed at this time, does not serve the national interest. The President concurred with the Departments recommendation and made that determination on January 18, 2012.
from the April 1, 2013 issue of the National Law Journal
http://www.pipelinelaw.com/files/2014/02/After_Keystone_A_question_of_presidential_permits.pdf
As the name suggests, presidential permits are a creation of the executive branch alone, with no
legislative authorization and limited judicial review to date. Presidential permits are intended to
provide executive branch review of trans-border facilities and commercial activities between the
United States and either Canada or Mexico. No statute authorizes their creation or use, and few
regulations govern their review or issuance.
...
In 1968, permitting authority for oil pipelines, among other facilities, was officially delegated to the State Department under President Lyndon Johnsons Executive Order 11,423 and amended by another executive order in 1994 to include requirements to consult with various federal departments. In 2004, an executive order by President George W. Bush established the State Departments procedures for reviewing presidential permit applications for oil pipelines. Those procedures include referral of the application and request for consulting agency reviews within 90 days and directions to approve those applications that serve the national interest.
The State Department is currently responsible for issuing presidential permits for oil pipelines, -while the Federal Energy Regulatory Commission (FERC) issues such permits for natural gas pipelines, and the Department of Energy (DOE) issues presidential permits for electric transmission lines. Both FERC and DOE have promulgated regulations governing their presidential permit process.
Section 1. (i)
The Secretary of State shall issue or deny the permit in accordance with the proposed determination...