"Obviously, I'm disappointed", Buckley told the Baltimore Sun.
The White House said Mr Trump ordered the flags lowered as soon as he learned of the Annapolis mayor's request. "Is there a cutoff for tragedy?" he asked.
The flag of the United States flies at half-staff over the White House in Washington, Tuesday, July 3, 2018, to honor the five people killed in the Annapolis, Md., shooting at the Capital Gazette newspaper.
Trump issued a proclamation Tuesday ordering the flags fly at half-staff through sundown. It was an attack on freedom of speech.
Shortly after the order was released Tuesday, Buckley told the Sun that the reversal was "the least respect we could give the journalists".
As The Capital Gazette reports, White House press secretary Sarah Huckabee-Sanders called Buckley Tuesday morning to inform him of Trump's decision.
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The city's mayor said the request was initially denied.
The victims included Rob Hiaasen, 59, the paper's assistant managing editor; Gerald Fischman, 61, the editorial page editor; Wendi Winters, 65, a features reporter; 56-year-old sports reporter John McNamara and Rebecca Smith, 34, a sales assistant.
Meanwhile, Jarrod W. Ramos, 38, has been charged with five counts of murder for last Thursday's shooting.
"At this point in time, it would start to polarise people and I don't want to make people angry", Mr Buckley, 55, who moved to the USA in 1992 and has become a successful restaurant owner in Annapolis, said.
However, since well before taking office, Trump has been openly antagonistic toward the press, calling it the "enemy of the American people," tweeting an image of him throttling a stand-in for a major media network - and, just three weeks ago, saying, "Our Country's biggest enemy is the Fake News so easily promulgated by fools!"