"We're not going to do the wind thing," Trump said at the time, calling them "big, ugly windmills" that were dangerous to wildlife.
New York's governor, Kathy Hochul, a Democrat, described the halt of Empire Wind 1 as "federal overreach" and said she would fight it "every step of the way".
Equinor, the Norwegian company that is leading the Empire Wind project, said in a statement: "We have decided to stop offshore construction of the project following the order."
"We will engage with the administration to find out why the order was issued after we had received all the permits previously."
Equinor acquired a lease of the site from the federal government in 2017 and, according to its website, the project was set to deliver 810 MW of energy into Brooklyn, powering 500,000 homes.
Trump has previously claimed, without evidence, that wind turbines kill whales.
Before becoming president, he battled - and ultimately failed - to stop the construction of a wind farm off the coast of his golf course in Aberdeenshire, Scotland.
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