TransCanada Corp.'s new application, which includes new proposed routes through Nebraska, comes after the U.S. government rejected the first application because it didn't include an alternative route to avoid an aquifer in Nebraska.
"The Department is committed to conducting a rigorous, transparent and thorough review," the State Department said in a news release.
The department said it would weigh factors including energy, health, environmental, cultural, economic and foreign policy concerns to determine whether the proposed pipeline is in the "national interest."
A third-party contractor will be hired to assist the department in its review, the release said.
TransCanada is seeking a permit for a section of the pipeline that would extend from the Canadian border and link to existing pipeline in Steele City, Neb., the department said.
Republicans have said the Obama administration has delayed approval of the pipeline in an election year to appease the environmental lobby.
Republicans, including presumptive presidential candidate Mitt Romney, have criticized the Obama administration's energy policies, while the administration says Republicans are attempting to force approval of the pipeline project before necessary review is done.