The Long Island City neighborhood was one of two locations the online retail giant selected last year after a long search for a second base, or "HQ2."
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Amazon had promised the sprawling complex in the borough of Queens would create 25,000 jobs in exchange for nearly $3 billion in state and city incentives.
But it withdrew the plans last week, blaming opposition from community leaders angry at the huge subsidies being offered to one of the world's most successful companies.
"I think it's a big loss," New York real estate mogul Trump said.
"I think if you look at the deal, the deal was not a great deal from the standpoint of they could have made a better deal than that, a much better deal, but still it's a loss to New York City."
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It marked a rare concession from the president, who has been a highly vocal critic of Amazon and its CEO Jeff Bezos, who also owns The Washington Post.
Trump has repeatedly accused the Post of lobbying for the company -- and claims the US Postal Service loses "billions of dollars" delivering Amazon packages.
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