The route proposed by TransCanada is east of the originally proposed route, which ran near an underground aquifer in Nebraska, CNN reported.
Environmentalists opposed to the project said the pipeline might leak into the water supply that provides much of the drinking water in Nebraska.
In January, President Barack Obama denied a permit for the 1,700-mile pipeline, a decision that has been contested by Republicans.
Obama then said in January he would approve the portion of the pipeline that runs from Cushing, Okla., to the Gulf.
"With this new route submitted and the state of Nebraska acting to move forward, the president is running out of excuses for blocking the Keystone pipeline any longer," House Speaker John Boehner, R-Ohio, said.
"With a veto-proof majority in the House supporting Keystone, the president is becoming increasingly isolated in his opposition to this job-creating energy project. He should listen to the voices of the American people and unlock the project so we can get Americans working and address high gas prices," he said.