Tow trucks and flood lights pulled up to the monument Thursday around 2 a.m., where large groups of supporters and protestors were still gathered.
The city began the process of removing the monuments late in 2015, but court challenges tied up the removal until now.
The dates and times of removal of the other two monuments-General Robert E. Lee and P.T. Beauregard-will be kept secret, according to a press release from Mayor Mitch Landrieu's office.
"This morning we continue our march to reconciliation by removing the Jefferson Davis Confederate statue from its pedestal of reverence", said Mayor Mitch Landrieu in a statement.
Like an earlier removal, this one was performed in the dark; Kaplan-Levenson says that's because of "death threats against city officials and contractors".More news: Thomas scores 53 as Celtics take 2-0 lead
Monument supporter Richard Marksbury said Monday that he has filed a lawsuit in state court to prevent the statue's removal.
The city removed the Battle of Liberty Place monument three weeks ago, which was erected by a white supremacist group to commemorate a deadly insurrection against New Orleans' racially integrated police department and government in 1874.
Be Civil - It's OK to have a difference in opinion but there's no need to be a jerk.
Another monument, the Battle of Liberty Place, was removed during the early morning hours. The term "Jefferson Davis" was also the top-trending term across the US on Thursday morning. The statue, nearly 17-feet tall and standing on a 68-foot pedestal, weighs more than 3 tons. In 2015, the city decide to remove them and in March, a US appeals court ruled that city had the right to proceed. Second, even if there was one, it is unlikely it would be powerful enough for policymakers to consider, because it would cause major political backlash, and it would be a significant departure from American tradition.
The Davis statue stood on top of a roughly 12-foot column, and depicted the Confederate president with his right arm outstretched, towering over the street also named after him.More news: Johnson confident this Players Championship will be different
New Orleans is a predominantly black city of almost 390,000.
People in favor of the removal of confederate era statues demonstrate across the street from the Jefferson Davis statue, in anticipation of its imminent removal in New Orleans, Thursday, May 11, 2017.
The Davis and Beauregard monuments are among four in New Orleans that critics have been pushing to have dismantled.
Around 4 a.m., two workers approached the Davis statue in a work lift and wrapped part of it in green plastic.
New Orleans will begin taking down Confederate statutes, becoming the latest Southern body to divorce itself from what some say are symbols of racism and intolerance.More news: French ex-prime minister Valls plans to back Macron in June elections
A last-ditch effort to block the removal of a monument to a Confederate general was rejected Wednesday by a Louisiana judge who turned away arguments that the city doesn't own the statue or the land on which it sits.
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