President Obama said he'd weigh the pipeline's national interest against its environmental footprint. Keystone XL would carry a denser type of crude oil from Canada, which is considered more carbon-intensive to produce than other types of oil.
A presidential permit is needed for the cross-border section of the pipeline. Construction on a domestic leg from Oklahoma is under way.
TransCanada sent a six-page letter to the State Department outlining what it said was "clarification" about the greenhouse gas emissions associated with the planned pipeline.
The Environmental Protection Agency said it was concerned about the possible emissions tied to the pipeline.
TransCanada said "the estimated increase in the average global temperature would be less than one one-hundred thousandth of a degree" because of crude oil production associated with the pipeline.
Furthermore, it said Thursday the pipeline itself would be powered by electric motors and therefore have few emissions of its own.
TransCanada says concerns over emissions fail to take into account the amount of Venezuelan and Mexican crude oil that would be displaced by Keystone XL.
"Keystone XL does not significantly exacerbate carbon emissions," the company said.