Indian Affairs and Northern Development minister Robert Nault announced the policy change Friday. NWT resources minister Jim Antoine said the territory supports the policy.
Under the policy, export of any amount of water over 40 litres is prohibited.
"This policy is intended to show that although there is abundant fresh water in the Northwest Territories, steps are being taken to ensure the resource will be protected," Nault said in a press release.
Nault said the policy was developed with input from the Northwest Territories and Nunavut.
"The conservation and protection of water requires the co-operation of all parties," Nault said.
"This is particularly true of river basins that cross boundaries."
The Mackenzie River is the largest drainage in the Northwest Territories and gathers water from Saskatchewan, Alberta, British Columbia and the Yukon.