The Dakota Access Pipeline, or DAPL, has sparked major protests near the Standing Rock Sioux Native American Indian reservation over fears it will disturb sacred ground and pollute drinking water.
Barack Obama blocked construction of a disputed segment of the pipeline in December in one of his last acts as President.
But Mr Trump has now signed executive actions to advance the 1,200-mile DAPL and another pipeline, the Keystone XL.
Mr Obama had previously rejected an application for the completion of the Keystone XL project in November 2015.
News two months ago that construction of the DAPL had been halted resulted in victory songs and joyous shrieks filling the air in the centre of the protest, the Oceti Sakowin camp.
Hundreds of Native Americans and climate activists had been camped out for months on the banks of the Missouri River, about 25 miles south of Bismarck, North Dakota.
There were fears at the time that celebrations would be short-lived because of the support Mr Trump showed on the campaign trail for fossil fuels.
The President told reporters on Tuesday that his administration would “renegotiate some of the terms” of both projects and would use it to create tens of thousands of jobs.
Mr Trump’s spokesman later explained that the renegotiation was to make sure the taxpayer gets the best value for money by ensuring that the firms due to make “millions” from the pipelines do not take advantage.
Sean Spicer said the President would work to make sure all parties, including the Native Americans, get something they want.
He said: “There’s a way that you can negotiate that, whether it’s the Native Americans and the concerns they have over some of the lands… the President has shown through his business life that he knows how to negotiate a great deal.
“He wants to make sure we get this back on track and done as quickly as possible.”
Mr Obama halted the proposed Keystone XL pipeline because he claimed it would prevent agreement on a climate change deal he regarded as a centrepiece of his environmental legacy.
The pipeline is expected to run from Canada to US refineries on the Gulf Coast.
Shortly after signing the order, Mr Trump banned staff at the Environmental Protection Agency from posting publicly on social media or talking to reporters.
It came as an operation to clean up more than 50,000 gallons of oils that leaked out of a pipeline onto an aboriginal reserve in Saskatchewan, just north of North Dakota in neighbouring Canada, continued.