Donald Trump "has authorized the Jones Act be waived for Puerto Rico", a statement said on Twitter.
Puerto Rico had pressed the US to lift the act, which limits shipping between coasts to US-flagged vessels.
The US territory is struggling with fuel, water and medical shortages one week after Hurricane Maria struck.
Federal emergency management officials and the US military have stepped up relief efforts as the scale of the island's crisis has become clear.
Many of its 3.4 million residents have been without electricity, reliable drinking supplies and other essentials since the storm struck.
The most powerful hurricane to hit Puerto Rico in nearly 90 years, Maria swept across the island last Wednesday.
The death toll was not as severe as Hurricane Irma - Maria claimed more than 30 lives in the Caribbean, including at least 16 in Puerto Rico.
But the storm knocked out the US territory's entire power grid, crippling its water and sewage treatment system.
The delivery of relief supplies has been hampered by roads rendered impassable by fallen trees or flooding, as well as communications outages.
Governor Ricardo Rossello called the devastation an unprecedented natural disaster.