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The waiver from the shipping law, which requires American-made and operated vessels to transport cargo between US ports, will only last for 10 days and goes into effect immediately, the Hill magazine reported.
"At @ricardorossello request, @POTUS has authorized the Jones Act to be waived for Puerto Rico. It will go into effect immediately," White House Press Secretary Sarah Huckabee Sanders wrote on Twitter, referring to Puerto Rico Governor Ricardo Rosselló.
Lawmakers in Congress since Monday had been pushing for a one-year waiver from the rules in an order to help speed up deliveries of food, fuel and other critical supplies to Puerto Rico, which was battered by two hurricanes last month.
Officials estimate that the island could be without power for six months.
The administration faced fierce backlash for not immediately lifting the law for Puerto Rico, after it issued a two-week waiver for Texas and Florida after hurricanes Harvey and Irma.
Mayor of San Juan, Puerto Rico's capital and largest city, praised the administration's decision, which she said could help bring down the costs of supplies and construction materials by nearly 33 per cent.
"Our cries for justice were heard," Carmen Yulín Cruz said. "The President did the right thing, and stood on the right side of history."
But she also warned that there are still thousands of containers sitting idle at the ports of San Juan, a problem she blamed on "jurisdictional" and bureaucratic issues.
Cruz called on the Federal Emergency Management Agency and the Governor to release the supplies to bigger and closer distribution centres.
"I have no jurisdiction over those ports," Cruz said. "Just like Trump heard the cry for justice to repeal the Jones Act, I ask you, I beg you, to repeat this and repeat this."