The announcement followed an environmental impact review from the U.S. State Department, which concluded the pipeline's impact on the environment would be "negligible to moderate".
Morris said the government must provide "new and relevant information regarding the risk of spills".
"This is a significant setback for TransCanada's Keystone XL pipeline project and big win for Indigenous defenders, the environment, and for the thousands of people who have been fighting this pipeline for almost a decade".
The decision is a blow to Trump, who signed an executive order after just two days in the White House to grant a permit for the construction of Keystone XL and Dakota Access, another bitterly-opposed project that sparked fierce protests form native American groups.
The judge added that the Trump administration had not adequately accounted for potential declines in oil prices, which have been depressed since the crash of 2014, and which would have a major effect on the long-term viability of such a project.
Judge Morris also said State didn't properly justify approving the pipeline in 2017 under Mr. Trump after rejecting it in 2015 under Mr. Obama. "The Trump administration tried to force this dirty pipeline project on the American people, but they can't ignore the threats it would pose to our clean water, our climate, and our communities".
Trump criticized the ruling, calling it a disgrace.
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The administration can appeal against the decision. TransCanada, the Calgary-based group behind the project, did not respond to request for comment early Friday morning.
In his ruling, the judge noted that the Department's analysis fell short of a "hard look" and requires a supplement to the 2014 supplemental environmental impact statement (SEIS) in order to comply with its obligations under National Environmental Policy Act. It has become one of the most controversial oil projects in North America, but it is also one of the most important for Canadian crude oil producers hit by a significant pipeline capacity shortage.
An AP map shows the proposed Keystone XL pipeline extension route.
The US stretch of line that needs to be built would be 875 miles (1,450 km) long. Native American groups in Montana and elsewhere fought the Keystone project as well, saying its route failed to adhere to historical treaty boundaries and would impinge on their water systems and sacred lands. Morris said that review was inadequate. The order came as a Canadian energy company prepared to assemble initial stages of the 1,200-mile long, cross-border project.
"An agency cannot simply disregard contrary or inconvenient factual determinations that it made in the past, any more than it can ignore inconvenient facts when it writes on a blank slate", he continued.